ENKIE
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ENKIE Overview
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2. API Reference
ENKIE
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B
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C
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D
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E
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F
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G
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I
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J
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K
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L
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M
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N
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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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Z
B
BmmKineticEstimator (class in enkie.estimators.bmm_kinetic_estimator)
C
chem_prop (enkie.dbs.metanetx.Metanetx property)
CHEM_PROP (enkie.dbs.metanetx.MnxFile attribute)
chem_xref (enkie.dbs.metanetx.Metanetx property)
CHEM_XREF (enkie.dbs.metanetx.MnxFile attribute)
clean_and_sort_protein_ids() (in module enkie.dbs.uniprot)
clear_enkie_cache() (in module enkie.storage)
cli
module
cmp_id_to_mnx_id (enkie.dbs.metanetx.Metanetx property)
COLUMNS (enkie.dbs.metanetx.Metanetx attribute)
combine_family_names() (in module enkie.dbs.uniprot)
COMMON (enkie.modular_rate_law.RateLawDenominator attribute)
compartment (enkie.miriam_metabolite.MiriamMetabolite property)
COMPARTMENT_ANY (in module enkie.compartment_parameters)
CompartmentParameters (class in enkie.compartment_parameters)
copy() (enkie.distributions.LogNormalDistribution method)
(enkie.distributions.LogUniformDistribution method)
(enkie.distributions.NormalDistribution method)
(enkie.distributions.UniformDistribution method)
core_cov (enkie.parameter_space.ParameterSpace property)
core_mean (enkie.parameter_space.ParameterSpace property)
core_to_all (enkie.parameter_space.ParameterSpace property)
cov (enkie.parameter_space.ParameterSpace property)
create() (enkie.io.cobra.EnzymeFactory method)
(enkie.io.cobra.EnzymeFactoryInterface method)
D
DEFAULT_I (in module enkie.constants)
DEFAULT_KCAT_MODEL (in module enkie.storage)
DEFAULT_KM_MODEL (in module enkie.storage)
DEFAULT_PH (in module enkie.constants)
DEFAULT_PHI (in module enkie.constants)
DEFAULT_PMG (in module enkie.constants)
DEFAULT_RATE_LAW_TYPE (in module enkie.modular_rate_law)
DEFAULT_RMSE (in module enkie.constants)
DEFAULT_SPONTANEOUS_GENES (in module enkie.constants)
DEFAULT_T (in module enkie.constants)
DIRECT_BINDING (enkie.modular_rate_law.RateLawDenominator attribute)
distribution_from_string() (in module enkie.distributions)
distribution_to_string() (in module enkie.distributions)
E
ec (enkie.enzyme.Enzyme property)
enkie
module
enkie.commons
module
enkie.compartment_parameters
module
enkie.constants
module
enkie.data
module
enkie.data.compartment_parameters
module
enkie.dbs
module
enkie.dbs.kegg
module
enkie.dbs.metanetx
module
enkie.dbs.uniprot
module
enkie.distributions
module
enkie.enzyme
module
enkie.estimators
module
enkie.estimators.bmm_kinetic_estimator
module
enkie.estimators.equilibrator_gibbs_estimator
module
enkie.estimators.fixed_kinetics_estimator
module
enkie.estimators.gibbs_estimator_interface
module
enkie.estimators.kinetic_parameter_types
module
enkie.estimators.kinetics_estimator_interface
module
enkie.estimators.parameter_balancer
module
enkie.io
module
enkie.io.cobra
module
enkie.metabolite
module
enkie.miriam_metabolite
module
enkie.miriam_reaction
module
enkie.modular_rate_law
module
enkie.parameter_space
module
enkie.reaction
module
enkie.singleton_meta
module
enkie.storage
module
enkie.utils
module
Enzyme (class in enkie.enzyme)
EnzymeFactory (class in enkie.io.cobra)
EnzymeFactoryInterface (class in enkie.io.cobra)
eq_api (enkie.estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator property)
EquilibratorGibbsEstimator (class in enkie.estimators.equilibrator_gibbs_estimator)
estimate_parameters() (enkie.estimators.parameter_balancer.ParameterBalancer method)
F
F (in module enkie.constants)
FAMILY_LEVELS (in module enkie.dbs.uniprot)
FixedKineticsEstimator (class in enkie.estimators.fixed_kinetics_estimator)
FORCE_DEPENDENT (enkie.modular_rate_law.RateLawDenominator attribute)
G
gene_ids (enkie.enzyme.Enzyme property)
get_cached_filepath() (in module enkie.storage)
get_compound_mass() (enkie.dbs.metanetx.Metanetx method)
get_data_path() (enkie.dbs.metanetx.Metanetx static method)
(in module enkie.storage)
get_dependence() (enkie.modular_rate_law.ModularRateLaw method)
get_dfg0_prime() (enkie.estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator method)
(enkie.estimators.gibbs_estimator_interface.GibbsEstimatorInterface method)
get_ec_to_rxn_mapping() (in module enkie.dbs.kegg)
get_internal_reaction_ids() (in module enkie.utils)
get_needed_metabolite_ids() (in module enkie.io.cobra)
get_parameters() (enkie.estimators.bmm_kinetic_estimator.BmmKineticEstimator method)
(enkie.estimators.fixed_kinetics_estimator.FixedKineticsEstimator method)
(enkie.estimators.kinetics_estimator_interface.KineticsEstimatorInterface method)
get_path() (in module enkie.utils)
gibbs_estimator (enkie.estimators.parameter_balancer.ParameterBalancer property)
GibbsEstimatorInterface (class in enkie.estimators.gibbs_estimator_interface)
I
I() (enkie.compartment_parameters.CompartmentParameters method)
id (enkie.metabolite.Metabolite property)
(enkie.modular_rate_law.ModularRateLaw property)
(enkie.reaction.Reaction property)
IDENTIFIER (enkie.dbs.metanetx.MetaboliteFormat attribute)
incorrect_metabolites (enkie.estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator property)
is_forward() (enkie.dbs.metanetx.Metanetx method)
J
join_protein_ids() (in module enkie.dbs.uniprot)
K
K_CAT_BACKWARD (enkie.estimators.kinetic_parameter_types.KineticParameterType attribute)
K_CAT_FORWARD (enkie.estimators.kinetic_parameter_types.KineticParameterType attribute)
K_M (enkie.estimators.kinetic_parameter_types.KineticParameterType attribute)
KineticParameterType (class in enkie.estimators.kinetic_parameter_types)
kinetics_estimator (enkie.estimators.parameter_balancer.ParameterBalancer property)
KineticsEstimatorInterface (class in enkie.estimators.kinetics_estimator_interface)
km_prior (enkie.estimators.parameter_balancer.ParameterBalancer property)
kv_prior (enkie.estimators.parameter_balancer.ParameterBalancer property)
L
lb (enkie.distributions.LogUniformDistribution property)
(enkie.distributions.UniformDistribution property)
load() (enkie.compartment_parameters.CompartmentParameters static method)
LOG10 (in module enkie.constants)
log_mean (enkie.distributions.LogNormalDistribution property)
log_std (enkie.distributions.LogNormalDistribution property)
LogNormalDistribution (class in enkie.distributions)
LogUniformDistribution (class in enkie.distributions)
M
main() (in module cli)
make_default_rate_laws() (in module enkie.io.cobra)
make_stoichiometric_matrix() (in module enkie.utils)
mean (enkie.distributions.NormalDistribution property)
(enkie.parameter_space.ParameterSpace property)
Metabolite (class in enkie.metabolite)
metabolite_ids (enkie.reaction.Reaction property)
metabolite_ids_kin (enkie.modular_rate_law.ModularRateLaw property)
MetaboliteFormat (class in enkie.dbs.metanetx)
metabolites (enkie.miriam_reaction.MiriamReaction property)
METABOLITES_CURATION_FILE (enkie.dbs.metanetx.Metanetx attribute)
metabolites_kin (enkie.modular_rate_law.ModularRateLaw property)
metadata (enkie.parameter_space.ParameterSpace property)
Metanetx (class in enkie.dbs.metanetx)
metanetx_id (enkie.miriam_metabolite.MiriamMetabolite property)
miriam_id (enkie.miriam_metabolite.MiriamMetabolite property)
(enkie.miriam_reaction.MiriamReaction property)
MiriamMetabolite (class in enkie.miriam_metabolite)
MiriamReaction (class in enkie.miriam_reaction)
mnx_id_to_formula_map (enkie.dbs.metanetx.Metanetx property)
mnx_id_to_mass (enkie.dbs.metanetx.Metanetx property)
MNX_URL_PREFIX (enkie.dbs.metanetx.Metanetx attribute)
MnxFile (class in enkie.dbs.metanetx)
ModularRateLaw (class in enkie.modular_rate_law)
module
cli
enkie
enkie.commons
enkie.compartment_parameters
enkie.constants
enkie.data
enkie.data.compartment_parameters
enkie.dbs
enkie.dbs.kegg
enkie.dbs.metanetx
enkie.dbs.uniprot
enkie.distributions
enkie.enzyme
enkie.estimators
enkie.estimators.bmm_kinetic_estimator
enkie.estimators.equilibrator_gibbs_estimator
enkie.estimators.fixed_kinetics_estimator
enkie.estimators.gibbs_estimator_interface
enkie.estimators.kinetic_parameter_types
enkie.estimators.kinetics_estimator_interface
enkie.estimators.parameter_balancer
enkie.io
enkie.io.cobra
enkie.metabolite
enkie.miriam_metabolite
enkie.miriam_reaction
enkie.modular_rate_law
enkie.parameter_space
enkie.reaction
enkie.singleton_meta
enkie.storage
enkie.utils
N
NAME (enkie.dbs.metanetx.MetaboliteFormat attribute)
name_to_mnx_compound_map (enkie.dbs.metanetx.Metanetx property)
nH (enkie.miriam_metabolite.MiriamMetabolite property)
NO_KM_MNX_IDS (enkie.modular_rate_law.ModularRateLaw attribute)
NoEstimateError
NormalDistribution (class in enkie.distributions)
num_independent_params (enkie.modular_rate_law.ModularRateLaw property)
num_metabolites (enkie.miriam_reaction.MiriamReaction property)
num_metabolites_kin (enkie.modular_rate_law.ModularRateLaw property)
P
ParameterBalancer (class in enkie.estimators.parameter_balancer)
ParameterSpace (class in enkie.parameter_space)
parse_enzymes() (in module enkie.io.cobra)
parse_family_df() (in module enkie.dbs.uniprot)
parse_family_string() (in module enkie.dbs.uniprot)
parse_metabolite_id() (in module enkie.io.cobra)
parse_metabolites() (in module enkie.io.cobra)
parse_reactions() (in module enkie.io.cobra)
pH() (enkie.compartment_parameters.CompartmentParameters method)
phi() (enkie.compartment_parameters.CompartmentParameters method)
pMg() (enkie.compartment_parameters.CompartmentParameters method)
POWER_LAW (enkie.modular_rate_law.RateLawDenominator attribute)
predict() (enkie.estimators.bmm_kinetic_estimator.BmmKineticEstimator method)
products (enkie.miriam_reaction.MiriamReaction property)
Q
Q (in module enkie.commons)
qrvector() (in module enkie.utils)
query_protein_data() (in module enkie.dbs.uniprot)
qvector() (in module enkie.utils)
R
R (in module enkie.constants)
RateLawDenominator (class in enkie.modular_rate_law)
reac_prop (enkie.dbs.metanetx.Metanetx property)
REAC_PROP (enkie.dbs.metanetx.MnxFile attribute)
reac_xref (enkie.dbs.metanetx.Metanetx property)
REAC_XREF (enkie.dbs.metanetx.MnxFile attribute)
Reaction (class in enkie.reaction)
reaction (enkie.modular_rate_law.ModularRateLaw property)
REACTIONS_CURATION_FILE (enkie.dbs.metanetx.Metanetx attribute)
rmse_inf (enkie.estimators.equilibrator_gibbs_estimator.EquilibratorGibbsEstimator property)
rxn_id_to_mnx_id (enkie.dbs.metanetx.Metanetx property)
S
S (enkie.miriam_reaction.MiriamReaction property)
sample() (enkie.parameter_space.ParameterSpace method)
SIMULTANEOUS_BINDING (enkie.modular_rate_law.RateLawDenominator attribute)
SingletonMeta (class in enkie.singleton_meta)
std (enkie.distributions.NormalDistribution property)
substrates (enkie.miriam_reaction.MiriamReaction property)
T
T() (enkie.compartment_parameters.CompartmentParameters method)
to_mnx_compound() (enkie.dbs.metanetx.Metanetx method)
to_mnx_reaction() (enkie.dbs.metanetx.Metanetx method)
to_reactions_idxs() (in module enkie.utils)
U
ub (enkie.distributions.LogUniformDistribution property)
(enkie.distributions.UniformDistribution property)
UniformDistribution (class in enkie.distributions)
uniprot_acs (enkie.enzyme.Enzyme property)
uniprot_fields (enkie.io.cobra.EnzymeFactoryInterface property)
UNKNOWN_ID (enkie.miriam_metabolite.MiriamMetabolite attribute)
Z
z (enkie.miriam_metabolite.MiriamMetabolite property)
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