Index A | B | C | D | E | F | G | I | J | K | L | M | N | O | P | R | S | T | U | V | W | Y A add2dict_unique() (in module cobramod.core.crossreferences) add_crossreferences() (in module cobramod) (in module cobramod.core.crossreferences) add_marker() (cobramod.core.pathway.JsonDictionary method) (cobramod.visualization.converter.JsonDictionary method) add_members() (cobramod.core.extension.Pathway method) (cobramod.core.pathway.Pathway method) (cobramod.Pathway method) add_metabolite() (cobramod.core.pathway.JsonDictionary method) (cobramod.visualization.converter.JsonDictionary method) (cobramod.visualization.converter.Reaction method) (cobramod.visualization.items.Reaction method) add_metabolites() (in module cobramod) (in module cobramod.core.creation) add_pathway() (in module cobramod) (in module cobramod.core.extension) add_pathway_from_data() (in module cobramod.core.extension) add_pathway_from_file() (in module cobramod.core.extension) add_pathway_from_strings() (in module cobramod.core.extension) add_reaction() (cobramod.core.pathway.JsonDictionary method) (cobramod.visualization.converter.JsonDictionary method) add_reactions() (in module cobramod) (in module cobramod.core.creation) add_reactions_to_model() (in module cobramod.utils) add_reactions_to_Pathway() (in module cobramod.core.extension) add_segment() (cobramod.visualization.converter.Reaction method) (cobramod.visualization.items.Reaction method) add_segments() (cobramod.core.pathway.JsonDictionary method) (cobramod.visualization.converter.JsonDictionary method) ARROWS (in module cobramod.utils) attributes (cobramod.retrieval.Data attribute) available_databases (in module cobramod.retrieval) B back() (in module cobramod.core.graph) BIOCYC (in module cobramod.retrieval) build_cross_references_xml() (in module cobramod.parsing.biocyc) build_lineal_graph() (in module cobramod.core.graph) build_metabolite() (in module cobramod.core.creation) (in module cobramod.utils) build_reaction_from_str() (in module cobramod.retrieval) build_reference() (in module cobramod.parsing.bigg) build_references() (in module cobramod.parsing.kegg) C CANVAS_HEIGHT (cobramod.core.pathway.JsonDictionary attribute) (cobramod.visualization.converter.JsonDictionary attribute) CANVAS_WIDTH (cobramod.core.pathway.JsonDictionary attribute) (cobramod.visualization.converter.JsonDictionary attribute) change_to_debug() (in module cobramod.debug) check_database_version() (cobramod.parsing.db_version.DataVersionConfigurator method) check_imbalance() (in module cobramod.utils) child_map() (in module cobramod.visualization.mapping) cobra_tolerance (in module cobramod.core.extension) cobramod module cobramod.core module cobramod.core.creation module cobramod.core.crossreferences module cobramod.core.extension module cobramod.core.genes module cobramod.core.graph module cobramod.core.pathway module cobramod.core.summary module cobramod.data module cobramod.debug module cobramod.error module cobramod.parsing module cobramod.parsing.bigg module cobramod.parsing.biocyc module cobramod.parsing.db_version module cobramod.parsing.kegg module cobramod.parsing.plantcyc module cobramod.parsing.solcyc module cobramod.retrieval module cobramod.test module cobramod.utils module cobramod.visualization module cobramod.visualization.converter module cobramod.visualization.debug module cobramod.visualization.escher module cobramod.visualization.force_graph module cobramod.visualization.items module cobramod.visualization.mapping module cobramod.visualization.pair module color (cobramod.visualization.escher.ReactionScale attribute) color_grading() (cobramod.core.pathway.JsonDictionary method) (cobramod.visualization.converter.JsonDictionary method) colors (in module cobramod.debug) compare_DictList() (in module cobramod.utils) compare_type() (in module cobramod.utils) confirm_metabolite() (in module cobramod.utils) confirm_sink() (in module cobramod.utils) convert_string_metabolite() (in module cobramod.core.creation) convert_to_transport() (in module cobramod.utils) create_object() (in module cobramod) (in module cobramod.core.creation) create_replacement() (in module cobramod.utils) cut_cycle() (in module cobramod.core.graph) cut_parents() (in module cobramod.core.graph) D Data (class in cobramod.retrieval) data_from_string() (in module cobramod.parsing.kegg) database (cobramod.retrieval.Data attribute) Databases (class in cobramod.retrieval) databases (in module cobramod.retrieval) DataModel (class in cobramod.core.extension) (class in cobramod.core.summary) DataVersionConfigurator (class in cobramod.parsing.db_version) db_configuration (in module cobramod.retrieval) debug_formatter (in module cobramod.visualization.debug) debug_handler (in module cobramod.debug) (in module cobramod.visualization.debug) debug_log (in module cobramod.core.creation) (in module cobramod.core.crossreferences) (in module cobramod.core.extension) (in module cobramod.core.genes) (in module cobramod.core.pathway) (in module cobramod.core.summary) (in module cobramod.debug) (in module cobramod.error) (in module cobramod.parsing.bigg) (in module cobramod.parsing.biocyc) (in module cobramod.parsing.db_version) (in module cobramod.parsing.kegg) (in module cobramod.parsing.plantcyc) (in module cobramod.parsing.solcyc) (in module cobramod.retrieval) (in module cobramod.utils) (in module cobramod.visualization.converter) (in module cobramod.visualization.debug) (in module cobramod.visualization.items) diff() (cobramod.core.extension.DataModel method) (cobramod.core.summary.DataModel method) E embedded_css (cobramod.core.pathway.EscherIntegration property) (cobramod.visualization.converter.EscherIntegration property) (cobramod.visualization.escher.EscherIntegration property) EscherIntegration (class in cobramod.core.pathway) (class in cobramod.visualization.converter) (class in cobramod.visualization.escher), [1] EXTENSIONS (in module cobramod.retrieval) F file_to_Data_class() (in module cobramod.retrieval) fill_matrix() (in module cobramod.visualization.mapping) filter_graph() (in module cobramod.core.graph) find_cycle() (in module cobramod.core.graph) find_intersection() (in module cobramod.utils) find_missing() (in module cobramod.core.graph) find_problem() (in module cobramod.core.extension) find_replacements() (in module cobramod.core.creation) find_url() (in module cobramod.parsing.bigg) fix_name() (in module cobramod.utils) ForceGraphIntegration (class in cobramod.core.pathway) (class in cobramod.visualization.force_graph), [1] format_matrix() (in module cobramod.visualization.mapping) format_str (in module cobramod.debug), [1] FORMAT_STR (in module cobramod.visualization.debug) formatter (in module cobramod.debug) formatter_file (in module cobramod.debug) FoundInPairError, [1] from_json() (cobramod.retrieval.Data class method) from_model() (cobramod.core.extension.DataModel class method) (cobramod.core.summary.DataModel class method) from_text() (cobramod.retrieval.Data class method) from_xml() (cobramod.retrieval.Data class method) G genes_to_reaction() (in module cobramod.core.genes) genome (cobramod.retrieval.Data attribute) get_all_values() (in module cobramod.visualization.mapping) get_arrow_position() (in module cobramod.utils) get_canvas() (cobramod.core.pathway.JsonDictionary method) (cobramod.visualization.converter.JsonDictionary method) get_credentials() (in module cobramod.utils) get_crossreferences() (in module cobramod.core.crossreferences) get_data() (in module cobramod) (in module cobramod.retrieval) get_database_version() (cobramod.parsing.db_version.DataVersionConfigurator method) get_direction_from_xml() (in module cobramod.parsing.biocyc) get_file_metabolites() (in module cobramod.core.creation) get_file_reactions() (in module cobramod.core.creation) get_files() (in module cobramod.retrieval) get_graph() (in module cobramod.parsing.biocyc) (in module cobramod.parsing.kegg) get_graph_dict() (in module cobramod.core.graph) (in module cobramod.visualization.mapping) get_index() (in module cobramod.visualization.mapping) get_key_dict() (in module cobramod.utils) get_local_databases() (cobramod.parsing.db_version.DataVersionConfigurator method) get_mapping() (in module cobramod.core.graph) (in module cobramod.visualization.converter) (in module cobramod.visualization.mapping) get_paths() (in module cobramod.core.graph) get_reac_prop_with_ec() (in module cobramod.core.crossreferences) get_reaction() (in module cobramod.core.creation) get_response() (in module cobramod.retrieval) GraphData (class in cobramod.visualization.force_graph) GraphKeyError, [1], [2] group (cobramod.visualization.force_graph.Nodes attribute) I id (cobramod.visualization.force_graph.Nodes attribute) identifier (cobramod.retrieval.Data attribute) inchikey2pubchem_cid() (in module cobramod.core.crossreferences) inform_new_sinks() (in module cobramod.utils) is_compound() (in module cobramod.utils) is_transport() (in module cobramod.utils) J json_dump() (cobramod.core.pathway.JsonDictionary method) (cobramod.visualization.converter.JsonDictionary method) JsonDictionary (class in cobramod.core.pathway) (class in cobramod.visualization.converter) K KEGG (in module cobramod.retrieval) kegg_info_to_version() (in module cobramod.utils) ko_generator() (in module cobramod.parsing.kegg) KO_LINK (in module cobramod.parsing.kegg) L Links (class in cobramod.visualization.force_graph) links (cobramod.visualization.force_graph.GraphData attribute) load_cache_from_disk() (in module cobramod.core.crossreferences) load_layout() (cobramod.core.pathway.ForceGraphIntegration method) (cobramod.visualization.force_graph.ForceGraphIntegration method), [1] log_dir (in module cobramod.debug) (in module cobramod.visualization.debug) log_path (in module cobramod.debug) (in module cobramod.visualization.debug) M map_json (cobramod.core.pathway.EscherIntegration attribute) (cobramod.visualization.converter.EscherIntegration attribute) (cobramod.visualization.escher.EscherIntegration attribute) map_metabolites() (cobramod.core.pathway.JsonDictionary method) (cobramod.visualization.converter.JsonDictionary method) map_name (cobramod.core.pathway.EscherIntegration attribute) (cobramod.visualization.converter.EscherIntegration attribute) (cobramod.visualization.escher.EscherIntegration attribute) marker() (cobramod.visualization.converter.Node method) (cobramod.visualization.items.Node method) metabolite() (cobramod.visualization.converter.Node method) (cobramod.visualization.items.Node method) metabolite_from_data() (in module cobramod.core.creation) metabolite_from_string() (in module cobramod.core.creation) metanetx2ec() (in module cobramod.core.crossreferences) mode (cobramod.retrieval.Data attribute) model (cobramod.core.pathway.ForceGraphIntegration property) (cobramod.visualization.force_graph.ForceGraphIntegration property), [1] model_convert() (in module cobramod) (in module cobramod.core.pathway) model_data (cobramod.core.pathway.EscherIntegration property) (cobramod.visualization.converter.EscherIntegration property) (cobramod.visualization.escher.EscherIntegration property) model_id (cobramod.retrieval.Data attribute) modify_graph() (cobramod.core.extension.Pathway method) (cobramod.core.pathway.Pathway method) (cobramod.Pathway method) module cobramod cobramod.core cobramod.core.creation cobramod.core.crossreferences cobramod.core.extension cobramod.core.genes cobramod.core.graph cobramod.core.pathway cobramod.core.summary cobramod.data cobramod.debug cobramod.error cobramod.parsing cobramod.parsing.bigg cobramod.parsing.biocyc cobramod.parsing.db_version cobramod.parsing.kegg cobramod.parsing.plantcyc cobramod.parsing.solcyc cobramod.retrieval cobramod.test cobramod.utils cobramod.visualization cobramod.visualization.converter cobramod.visualization.debug cobramod.visualization.escher cobramod.visualization.force_graph cobramod.visualization.items cobramod.visualization.mapping cobramod.visualization.pair N never_ask_before_quit (cobramod.core.pathway.EscherIntegration attribute) (cobramod.visualization.converter.EscherIntegration attribute) (cobramod.visualization.escher.EscherIntegration attribute) Node (class in cobramod.visualization.converter) (class in cobramod.visualization.items) NodeAttributeError, [1] NoDelimiter Nodes (class in cobramod.visualization.force_graph) nodes (cobramod.visualization.force_graph.GraphData attribute) NoGeneInformation NoIntersectFound non_zero_core() (in module cobramod.core.extension) O options (cobramod.core.pathway.EscherIntegration property) (cobramod.visualization.converter.EscherIntegration property) (cobramod.visualization.escher.EscherIntegration property) P PairDictionary (class in cobramod.visualization.items) (class in cobramod.visualization.pair) parse() (cobramod.retrieval.Data method) parse_genes() (in module cobramod.parsing.bigg) (in module cobramod.parsing.biocyc) (in module cobramod.parsing.kegg) parse_ko_to_genes() (in module cobramod.parsing.kegg) parse_metabolite_attributes() (in module cobramod.parsing.bigg) (in module cobramod.parsing.biocyc) (in module cobramod.parsing.kegg) parse_pathway_attributes() (in module cobramod.parsing.biocyc) (in module cobramod.parsing.kegg) parse_reaction_attributes() (in module cobramod.parsing.bigg) (in module cobramod.parsing.biocyc) (in module cobramod.parsing.kegg) path (cobramod.retrieval.Data attribute) Pathway (class in cobramod), [1] (class in cobramod.core.extension) (class in cobramod.core.pathway) PatternNotFound PMN (in module cobramod.retrieval) Position (in module cobramod.visualization.converter) R R_HEIGHT (cobramod.core.pathway.JsonDictionary attribute) (cobramod.visualization.converter.JsonDictionary attribute) R_WIDTH (cobramod.core.pathway.JsonDictionary attribute) (cobramod.visualization.converter.JsonDictionary attribute) Reaction (class in cobramod.visualization.converter) (class in cobramod.visualization.items) reaction_data (cobramod.core.pathway.EscherIntegration attribute) (cobramod.core.pathway.JsonDictionary attribute) (cobramod.visualization.converter.EscherIntegration attribute) (cobramod.visualization.converter.JsonDictionary attribute) (cobramod.visualization.escher.EscherIntegration attribute) reaction_from_string() (in module cobramod.core.creation) reaction_is_minimize() (in module cobramod.utils) reaction_scale (cobramod.core.pathway.EscherIntegration attribute) (cobramod.visualization.converter.EscherIntegration attribute) (cobramod.visualization.escher.EscherIntegration attribute) reaction_str_from_xml() (in module cobramod.parsing.biocyc) reaction_styles (cobramod.core.pathway.EscherIntegration attribute) (cobramod.visualization.converter.EscherIntegration attribute) (cobramod.visualization.escher.EscherIntegration attribute) ReactionScale (class in cobramod.visualization.escher), [1] read_lines() (in module cobramod.utils) recursive_flux_test() (in module cobramod.core.extension) remove_avoid_reactions() (in module cobramod.core.extension) retrieve_gene_information() (in module cobramod.parsing.biocyc) (in module cobramod.parsing.plantcyc) (in module cobramod.parsing.solcyc) retrieve_kegg_genes() (in module cobramod.parsing.kegg) return_cycles() (in module cobramod.core.graph) S save_html() (cobramod.core.pathway.EscherIntegration method) (cobramod.visualization.converter.EscherIntegration method) (cobramod.visualization.escher.EscherIntegration method), [1] save_layout() (cobramod.core.pathway.ForceGraphIntegration method) (cobramod.visualization.force_graph.ForceGraphIntegration method), [1] Segment (class in cobramod.visualization.items) set_database_version() (cobramod.parsing.db_version.DataVersionConfigurator method) set_pair() (cobramod.visualization.items.PairDictionary method) (cobramod.visualization.pair.PairDictionary method) size (cobramod.visualization.escher.ReactionScale attribute) SOLCYC (in module cobramod.retrieval) solution (cobramod.core.pathway.ForceGraphIntegration property) (cobramod.visualization.force_graph.ForceGraphIntegration property), [1] solution() (cobramod.core.extension.Pathway method) (cobramod.core.pathway.Pathway method) (cobramod.Pathway method) source (cobramod.visualization.force_graph.Links property) stream_handler (in module cobramod.debug) string_to_reaction() (in module cobramod.core.creation) summarize() (in module cobramod.core.extension) summary() (in module cobramod.core.summary) SuperpathwayException T target (cobramod.visualization.force_graph.Links property) test_non_zero_flux() (in module cobramod) (in module cobramod.core.extension) textbook (in module cobramod.test) textbook_biocyc (in module cobramod.test) textbook_biocyc_groups (in module cobramod.test) textbook_kegg (in module cobramod.test) TIME_STR (in module cobramod.debug) (in module cobramod.visualization.debug) to_csv() (cobramod.core.extension.DataModel method) (cobramod.core.summary.DataModel method) to_dict() (cobramod.visualization.force_graph.GraphData method) to_excl() (cobramod.core.extension.DataModel method) (cobramod.core.summary.DataModel method) to_json() (cobramod.visualization.force_graph.GraphData method) (cobramod.visualization.force_graph.Links method) (cobramod.visualization.force_graph.Nodes method) to_txt() (cobramod.core.extension.DataModel method) (cobramod.core.summary.DataModel method) transpose() (in module cobramod.visualization.converter) (in module cobramod.visualization.mapping) type (cobramod.visualization.escher.ReactionScale attribute) U UnbalancedReaction unformatted_matrix() (in module cobramod.visualization.mapping) UserInterruption V value (cobramod.visualization.escher.ReactionScale attribute) (cobramod.visualization.force_graph.Links attribute) verify_paths() (in module cobramod.core.graph) version (cobramod.retrieval.Data attribute) visualize() (cobramod.core.extension.Pathway method) (cobramod.core.pathway.JsonDictionary method) (cobramod.core.pathway.Pathway method) (cobramod.Pathway method), [1] (cobramod.visualization.converter.JsonDictionary method) W write() (in module cobramod.retrieval) write_to_file() (in module cobramod.utils) WrongDataError WrongParserError, [1] WrongSyntax Y yield_reaction_from_list() (in module cobramod.core.extension)