Index

_

_add_reaction_markers() (fluxpy.illustrations.build_escher_map.JsonDictionary method) (in module fluxpy.illustrations.build_escher_map) _check_if_modelseed_model() (in module fluxpy.utils.model) _cmap() (in module fluxpy.constants) _color2np_rgb() (in module fluxpy.illustrations.build_escher_map) _Conversions (class in fluxpy.utils.model) _convert_dash_cytoscape_to_cx2() (in module fluxpy.illustrations.illustrations) _convert_list_to_binary() (in module fluxpy.utils.utils) _convert_single_element_set() (in module fluxpy.utils.utils) _convert_string() (in module fluxpy.illustrations.build_escher_map) _divide_values() (in module fluxpy.illustrations.build_escher_map) _ExportedGraph (class in fluxpy.illustrations.illustrations) _find_shared() (fluxpy.illustrations.build_escher_map.JsonDictionary method) _generate_points_inside_cone() (in module fluxpy.illustrations.illustrations) _get_last_number() (fluxpy.illustrations.build_escher_map.JsonDictionary method) (in module fluxpy.illustrations.build_escher_map)

_get_matrix_reactions() (fluxpy.illustrations.build_escher_map.JsonDictionary method) _get_products() (fluxpy.illustrations.build_escher_map.JsonDictionary method) _get_set() (fluxpy.illustrations.build_escher_map.JsonDictionary method) (in module fluxpy.illustrations.build_escher_map) _met_ids_to_met_names() (fluxpy.utils.model.NameIdConverter method) (fluxpy.utils.NameIdConverter method) _met_names_to_met_ids() (fluxpy.utils.model.NameIdConverter method) (fluxpy.utils.NameIdConverter method) _overview (fluxpy.illustrations.build_escher_map.JsonDictionary attribute) _perform_recursive() (in module fluxpy.utils.utils) _react_ids_to_react_names() (fluxpy.utils.model.NameIdConverter method) (fluxpy.utils.NameIdConverter method) _react_names_to_react_ids() (fluxpy.utils.model.NameIdConverter method) (fluxpy.utils.NameIdConverter method) _reset() (fluxpy.illustrations.build_escher_map.JsonDictionary method)

A

add_marker() (fluxpy.illustrations.build_escher_map.JsonDictionary method) (in module fluxpy.illustrations.build_escher_map) add_metabolite() (fluxpy.illustrations.build_escher_map.JsonDictionary method)

add_reaction() (fluxpy.illustrations.build_escher_map.JsonDictionary method) add_segments() (fluxpy.illustrations.build_escher_map.JsonDictionary method) all_namespaces (in module fluxpy.utils.model) auto_decorate() (in module fluxpy.auto_decorator)

B

BIGG2MNX (in module fluxpy.constants) BIGG_BUILDING_BLOCLS (in module fluxpy.constants)

BIGG_COFACTORS (in module fluxpy.constants) build_markers() (in module fluxpy.illustrations.build_escher_map)

C

CANVAS_HEIGHT (fluxpy.illustrations.build_escher_map.JsonDictionary attribute), [1] CANVAS_WIDTH (fluxpy.illustrations.build_escher_map.JsonDictionary attribute), [1] CMAP (in module fluxpy.constants) cofactors_abundance() (fluxpy.utils.model.CofactorSpecificity method) CofactorSpecificity (class in fluxpy.utils.model) color_grading() (fluxpy.illustrations.build_escher_map.JsonDictionary method) column (fluxpy.illustrations.build_escher_map.Position attribute) compare_model_pair() (fluxpy.utils.CompareModels method) (fluxpy.utils.model.CompareModels method)

CompareModels (class in fluxpy.utils) (class in fluxpy.utils.model) COMPLETE_MODEL (in module fluxpy.constants) convert (fluxpy.utils.model.NameIdConverter attribute) (fluxpy.utils.NameIdConverter attribute) convert_gbk_to_faa() (in module fluxpy.utils) (in module fluxpy.utils.format) current_file_path (in module fluxpy.constants) cx2_graph (fluxpy.illustrations.illustrations._ExportedGraph attribute)

D

dash_graph (fluxpy.illustrations.illustrations._ExportedGraph attribute)

decorate_all_functions_in_module() (in module fluxpy.auto_decorator)

E

EXT_DATA (in module fluxpy.constants) extract_dynamic_value() (in module kegg_pairs)

extract_model_namespace() (in module fluxpy.utils) (in module fluxpy.utils.utils)

F

filter_reactions() (fluxpy.utils.model.CofactorSpecificity method) find_connected_components() (in module fluxpy.utils.utils) find_first_winning_sublist_with_losers() (in module fluxpy.utils.utils) find_reactants_products_cofactors() (fluxpy.utils.model.CofactorSpecificity method) find_reactions_combinations() (fluxpy.utils.model.CofactorSpecificity method) flux_cone_example() (in module fluxpy.illustrations) (in module fluxpy.illustrations.illustrations) flux_solution (fluxpy.illustrations.build_escher_map.JsonDictionary attribute) fluxpy module fluxpy.auto_decorator module fluxpy.constants module fluxpy.decorators module fluxpy.illustrations module

fluxpy.illustrations.build_escher_map module fluxpy.illustrations.illustrations module fluxpy.stats module fluxpy.stats.extract_stats_from_solution module fluxpy.utils module fluxpy.utils.analysis module fluxpy.utils.format module fluxpy.utils.model module fluxpy.utils.utils module

G

get_canvas() (fluxpy.illustrations.build_escher_map.JsonDictionary method) get_nutrients_gradient() (in module fluxpy.utils) (in module fluxpy.utils.analysis) get_reactions_producing_a_met() (in module fluxpy.utils) (in module fluxpy.utils.analysis)

get_rxns_producing_consuming_met() (in module fluxpy.utils) (in module fluxpy.utils.utils) go_for_markers_for_a_reaction() (in module fluxpy.illustrations.build_escher_map) graph (fluxpy.illustrations.build_escher_map.JsonDictionary attribute)

I

isIndex (fluxpy.utils.model.NameIdConverter attribute) (fluxpy.utils.NameIdConverter attribute)

J

json_dump() (fluxpy.illustrations.build_escher_map.JsonDictionary method)

JsonDictionary (class in fluxpy.illustrations.build_escher_map)

K

kegg_pairs module

M

map_metabolites() (fluxpy.illustrations.build_escher_map.JsonDictionary method) map_namespace_to_ModelSEEDDatabase() (in module fluxpy.utils) (in module fluxpy.utils.model) map_to_namespace() (in module fluxpy.utils) (in module fluxpy.utils.model) merge_connected_combinations() (fluxpy.utils.model.CofactorSpecificity method) met_map_df (fluxpy.utils.model.NameIdConverter attribute) (fluxpy.utils.NameIdConverter attribute) METABOLITE_IDS (fluxpy.utils.model._Conversions attribute) METABOLITE_NAMES (fluxpy.utils.model._Conversions attribute) metabolites_df (fluxpy.utils.CompareModels attribute) (fluxpy.utils.model.CompareModels attribute) model (fluxpy.utils.model.CofactorSpecificity attribute) (fluxpy.utils.model.NameIdConverter attribute) (fluxpy.utils.NameIdConverter attribute) model_names (fluxpy.utils.CompareModels attribute) (fluxpy.utils.model.CompareModels attribute) Models (class in fluxpy.utils) (class in fluxpy.utils.model)

models (fluxpy.utils.CompareModels attribute) (fluxpy.utils.model.CompareModels attribute) MODELSEED_COFACTORS (in module fluxpy.constants) module fluxpy fluxpy.auto_decorator fluxpy.constants fluxpy.decorators fluxpy.illustrations fluxpy.illustrations.build_escher_map fluxpy.illustrations.illustrations fluxpy.stats fluxpy.stats.extract_stats_from_solution fluxpy.utils fluxpy.utils.analysis fluxpy.utils.format fluxpy.utils.model fluxpy.utils.utils kegg_pairs

N

NameIdConverter (class in fluxpy.utils) (class in fluxpy.utils.model) namespace (fluxpy.utils.CompareModels attribute) (fluxpy.utils.model.CompareModels attribute)

NestedDataFrameType (in module fluxpy.utils.utils) nonzero_fluxes() (in module fluxpy.utils) (in module fluxpy.utils.utils) number_of_models (fluxpy.utils.CompareModels attribute) (fluxpy.utils.model.CompareModels attribute)

O

order_cofactors_by_abundance() (in module fluxpy.utils.utils)

P

parent_folder (in module fluxpy.constants) parse_qfca() (in module fluxpy.utils) (in module fluxpy.utils.analysis) plot_nutrients_gradient() (in module fluxpy.illustrations) (in module fluxpy.illustrations.illustrations) plot_prod_env_3D() (in module fluxpy.illustrations) (in module fluxpy.illustrations.illustrations)

plot_ranging_medium_compounds() (in module fluxpy.illustrations) (in module fluxpy.illustrations.illustrations) Position (class in fluxpy.illustrations.build_escher_map) print_doc_on_typeerror() (in module fluxpy.decorators) producing_or_consuming_a_met() (in module fluxpy.utils) (in module fluxpy.utils.analysis)

Q

qcfa_subgraphs() (in module fluxpy.illustrations) (in module fluxpy.illustrations.illustrations)

QFCA_STYLE (in module fluxpy.constants)

R

R_HEIGHT (fluxpy.illustrations.build_escher_map.JsonDictionary attribute), [1] R_WIDTH (fluxpy.illustrations.build_escher_map.JsonDictionary attribute), [1] react_map_df (fluxpy.utils.model.NameIdConverter attribute) (fluxpy.utils.NameIdConverter attribute) reaction_data (fluxpy.illustrations.build_escher_map.JsonDictionary attribute) REACTION_IDS (fluxpy.utils.model._Conversions attribute) REACTION_NAMES (fluxpy.utils.model._Conversions attribute) reaction_scale (fluxpy.illustrations.build_escher_map.JsonDictionary attribute) reaction_strings (fluxpy.illustrations.build_escher_map.JsonDictionary attribute)

reactions_df (fluxpy.utils.CompareModels attribute) (fluxpy.utils.model.CompareModels attribute) remove_reactions() (fluxpy.utils.model.CofactorSpecificity method) res (fluxpy.utils.CompareModels attribute) (fluxpy.utils.model.CompareModels attribute) root_folder (in module fluxpy.constants) row (fluxpy.illustrations.build_escher_map.Position attribute) run_convert() (fluxpy.utils.model.NameIdConverter method) (fluxpy.utils.NameIdConverter method)

S

samples_on_qfca() (in module fluxpy.utils) (in module fluxpy.utils.analysis) SEED2MNX (in module fluxpy.constants) shared_metabolites() (fluxpy.utils.CompareModels method) (fluxpy.utils.model.CompareModels method)

shared_reactions() (fluxpy.utils.CompareModels method) (fluxpy.utils.model.CompareModels method) slope_in_prod_env() (in module fluxpy.stats) (in module fluxpy.stats.extract_stats_from_solution) sync_with_medium() (in module fluxpy.utils) (in module fluxpy.utils.model)

T

to (fluxpy.utils.model.NameIdConverter attribute) (fluxpy.utils.NameIdConverter attribute) trace_path_with_backtracking_iterative() (in module fluxpy.utils) (in module fluxpy.utils.analysis)

track_metabolite_pathways() (in module fluxpy.utils.utils) transform_dict() (in module kegg_pairs) transform_values() (in module kegg_pairs)

U

unique_metabolites() (fluxpy.utils.CompareModels method) (fluxpy.utils.model.CompareModels method)

unique_reactions() (fluxpy.utils.CompareModels method) (fluxpy.utils.model.CompareModels method)

V

visualize() (fluxpy.illustrations.build_escher_map.JsonDictionary method)

X

X (fluxpy.illustrations.build_escher_map.JsonDictionary attribute)

Y

Y (fluxpy.illustrations.build_escher_map.JsonDictionary attribute)