Index

_

__getitem__() (geckopy.protein.Kcats method) __iter__() (geckopy.protein.Kcats method) __repr__() (geckopy.protein.Kcats method) __setitem__() (geckopy.protein.Kcats method) __setstate__() (geckopy.Model method) (geckopy.model.Model method) (geckopy.Protein method) (geckopy.protein.Protein method) __str__() (geckopy.Protein method) (geckopy.protein.Protein method) _LC_vars (geckopy.integration.pytfa.ThermoModel attribute)

_metabolites() (geckopy.Protein property) (geckopy.protein.Protein property) _model_warn() (geckopy.protein.Kcats method) _populate_solver() (geckopy.Model method) (geckopy.model.Model method) _prepare_pseudometabolites_dfg() (in module geckopy.integration.pytfa) _repr_html_() (geckopy.Protein method) (geckopy.protein.Protein method) _set_id_with_model() (geckopy.Protein method) (geckopy.protein.Protein method) _update() (geckopy.protein.Kcats method)

A

adapt_gecko_to_thermo() (in module geckopy.integration.pytfa) add_boundary() (geckopy.Model method) (geckopy.model.Model method) add_concentration() (geckopy.Protein method) (geckopy.protein.Protein method) add_pool() (geckopy.Model method) (geckopy.model.Model method)

add_protein() (geckopy.reaction.Reaction method) add_proteins() (geckopy.Model method) (geckopy.model.Model method) add_reactions() (geckopy.Model method) (geckopy.model.Model method) apply_proteomics_elastic_relaxation() (in module geckopy.experimental.relaxation) apply_proteomics_relaxation() (in module geckopy.experimental.relaxation)

B

bounds() (geckopy.Protein property) (geckopy.protein.Protein property)

C

charge (geckopy.Protein attribute) (geckopy.protein.Protein attribute) concentration (geckopy.Protein attribute) (geckopy.protein.Protein attribute) concentration() (geckopy.Protein property) (geckopy.protein.Protein property) config (in module geckopy.protein)

constrain_pool() (geckopy.Model method) (geckopy.model.Model method) contribution (geckopy.Protein attribute) (geckopy.protein.Protein attribute) contribution() (geckopy.Protein property) (geckopy.protein.Protein property) copy() (geckopy.Model method) (geckopy.model.Model method)

E

elastic_upper_relaxation() (in module geckopy.experimental.relaxation)

extract_proteins() (in module geckopy.experimental.molecular_weights)

F

flux() (geckopy.Protein property) (geckopy.protein.Protein property) flux_variability_analysis() (in module geckopy) (in module geckopy.flux_analysis) formula (geckopy.Protein attribute) (geckopy.protein.Protein attribute) forward_variable() (geckopy.Protein property) (geckopy.protein.Protein property)

from_cobra() (geckopy.Model method) (geckopy.model.Model method) from_copy_number() (in module geckopy.experimental) (in module geckopy.experimental.experimental) from_metabolite() (geckopy.Protein method) (geckopy.protein.Protein method) from_mmol_gDW() (in module geckopy.experimental) (in module geckopy.experimental.experimental)

G

geckopy module geckopy.experimental module geckopy.experimental.experimental module geckopy.experimental.molecular_weights module geckopy.experimental.relaxation module geckopy.flux_analysis module geckopy.integration module geckopy.integration.pytfa module geckopy.integration.relaxation module geckopy.io module

geckopy.model module geckopy.protein module geckopy.reaction module genes (geckopy.Model attribute) (geckopy.model.Model attribute) get_protein_bottlenecks() (in module geckopy.flux_analysis) get_protein_usage_by_reaction_rate() (in module geckopy.flux_analysis) get_thermo_coverage() (in module geckopy.integration.pytfa) get_thermo_reactions() (in module geckopy.integration.pytfa) get_total_measured_proteins() (geckopy.Model method) (geckopy.model.Model method) get_uniprot() (in module geckopy.experimental.molecular_weights) get_upper_relaxation() (in module geckopy.experimental.relaxation) groups (geckopy.Model attribute) (geckopy.model.Model attribute)

I

id (geckopy.Protein attribute) (geckopy.protein.Protein attribute)

items() (geckopy.protein.Kcats method)

K

Kcats (class in geckopy.protein) kcats (geckopy.Protein attribute) (geckopy.protein.Protein attribute)

keys() (geckopy.protein.Kcats method)

L

LC_vars() (geckopy.integration.pytfa.ThermoModel property) limit_proteins() (in module geckopy.experimental) (in module geckopy.experimental.experimental) LOGGER (in module geckopy.integration.pytfa) (in module geckopy.integration.relaxation) (in module geckopy.model) (in module geckopy.protein)

lower_bound (geckopy.Protein attribute) (geckopy.protein.Protein attribute)

M

M (in module geckopy.integration.relaxation) metabolites (geckopy.Model attribute) (geckopy.model.Model attribute) metabolites() (geckopy.Protein property) (geckopy.protein.Protein property) MIN_ELASTIC_SUM (geckopy.experimental.relaxation.Objective_rule attribute) MIN_ELASTIC_SUM_OBJECTIVE (geckopy.experimental.relaxation.Objective_rule attribute) MIN_MILP_COUNT (geckopy.experimental.relaxation.Objective_rule attribute) Model (class in geckopy) (class in geckopy.model) model() (geckopy.Protein property) (geckopy.protein.Protein property) module geckopy geckopy.experimental geckopy.experimental.experimental geckopy.experimental.molecular_weights geckopy.experimental.relaxation geckopy.flux_analysis geckopy.integration geckopy.integration.pytfa geckopy.integration.relaxation geckopy.io geckopy.model geckopy.protein geckopy.reaction

mw (geckopy.Protein attribute) (geckopy.protein.Protein attribute)

N

name (geckopy.Protein attribute) (geckopy.protein.Protein attribute)

O

objective_coefficient() (geckopy.Protein property) (geckopy.protein.Protein property)

Objective_rule (class in geckopy.experimental.relaxation) optimize() (geckopy.Model method) (geckopy.model.Model method)

P

parse_mw() (in module geckopy.experimental.molecular_weights) pfba_protein() (in module geckopy.flux_analysis) products() (geckopy.Protein property) (geckopy.protein.Protein property) PROT_CUE_DATA (in module geckopy.integration.pytfa) PROT_DATA (in module geckopy.integration.pytfa)

Protein (class in geckopy) (class in geckopy.protein) protein_variability_analysis() (in module geckopy.flux_analysis) proteins (geckopy.Model attribute) (geckopy.model.Model attribute) proteins() (geckopy.reaction.Reaction property)

R

rate_kcat_concentration() (in module geckopy.flux_analysis) reactants() (geckopy.Protein property) (geckopy.protein.Protein property) Reaction (class in geckopy.reaction) reactions (geckopy.Model attribute) (geckopy.model.Model attribute) reactions() (geckopy.Protein property) (geckopy.protein.Protein property) read_sbml_ec_model() (in module geckopy.io)

relax_proteomics_greedy() (in module geckopy.experimental.relaxation) relax_thermo_concentrations_proteins() (in module geckopy.integration) (in module geckopy.integration.relaxation) relax_thermo_proteins() (in module geckopy.integration) (in module geckopy.integration.relaxation) reverse_id() (geckopy.Protein property) (geckopy.protein.Protein property) reverse_variable() (geckopy.Protein property) (geckopy.protein.Protein property)

S

solution (geckopy.Model attribute) (geckopy.model.Model attribute)

suscribe_to_pool() (geckopy.Protein method) (geckopy.protein.Protein method)

T

ThermoModel (class in geckopy.integration.pytfa)

translate_model_mnx_to_seed() (in module geckopy.integration.pytfa)

U

UNIPROT_PATTERN (in module geckopy.protein) unsuscribe_to_pool() (geckopy.Protein method) (geckopy.protein.Protein method) update_variable_bounds() (geckopy.Protein method) (geckopy.protein.Protein method)

upper_bound (geckopy.Protein attribute) (geckopy.protein.Protein attribute) upper_bound() (geckopy.Protein property) (geckopy.protein.Protein property)

V

values() (geckopy.protein.Kcats method)

W

write_sbml_ec_model() (in module geckopy.io)

write_thermodb() (in module geckopy.integration.pytfa)