Index

A

absent_and_specific_reactions() (in module padmet.utils.exploration.dendrogram_reactions_distance) add_collapsible() (in module padmet.utils.connection.wikiGenerator) add_delete_rxn() (in module padmet.utils.management.manual_curation) add_dendrogram_node_label() (in module padmet.utils.exploration.dendrogram_reactions_distance) add_element_to_tree() (in module padmet.utils.connection.get_metacyc_ontology) add_ga() (in module padmet.utils.connection.sbmlGenerator)

add_kegg_pwy() (in module padmet.utils.connection.biggAPI_to_padmet) (in module padmet.utils.connection.modelSeed_to_padmet) add_property() (in module padmet.utils.connection.wikiGenerator) analysisOutput() (in module padmet.utils.exploration.prot2genome) ascii_replace() (in module padmet.utils.sbmlPlugin) asp_synt() (in module padmet.utils.connection.padmet_to_asp)

B

biggAPI_to_padmet() (in module padmet.utils.connection.biggAPI_to_padmet)

biggAPI_to_padmet_cli() (in module padmet.utils.connection.biggAPI_to_padmet)

C

change_compart() (padmet.classes.padmetSpec.PadmetSpec method) check() (in module padmet.utils.connection.sbmlGenerator) check_ids() (in module padmet.utils.connection.check_orthology_input) check_orthology_input() (in module padmet.utils.connection.check_orthology_input) check_orthology_input_cli() (in module padmet.utils.connection.check_orthology_input) check_sbml_db() (in module padmet.utils.exploration.convert_sbml_db) classes_parser() (in module padmet.utils.connection.pgdb_to_padmet) cleanTmp() (in module padmet.utils.exploration.prot2genome) Closing (padmet.utils.gbr.Type attribute) Command (class in padmet.utils.gbr) command_help() (in module padmet.utils.connection.biggAPI_to_padmet) (in module padmet.utils.connection.check_orthology_input) (in module padmet.utils.connection.enhanced_meneco_output) (in module padmet.utils.connection.extract_orthofinder) (in module padmet.utils.connection.extract_rxn_with_gene_assoc) (in module padmet.utils.connection.gbk_to_faa) (in module padmet.utils.connection.gene_to_targets) (in module padmet.utils.connection.get_metacyc_ontology) (in module padmet.utils.connection.metexploreviz_export) (in module padmet.utils.connection.modelSeed_to_padmet) (in module padmet.utils.connection.padmet_to_asp) (in module padmet.utils.connection.padmet_to_matrix) (in module padmet.utils.connection.padmet_to_padmet) (in module padmet.utils.connection.padmet_to_tsv) (in module padmet.utils.connection.pgdb_to_padmet) (in module padmet.utils.connection.sbml_to_curation_form) (in module padmet.utils.connection.sbml_to_padmet) (in module padmet.utils.connection.sbml_to_sbml) (in module padmet.utils.connection.sbmlGenerator) (in module padmet.utils.connection.wikiGenerator) (in module padmet.utils.exploration.compare_padmet) (in module padmet.utils.exploration.compare_sbml) (in module padmet.utils.exploration.compare_sbml_padmet) (in module padmet.utils.exploration.convert_sbml_db) (in module padmet.utils.exploration.dendrogram_reactions_distance) (in module padmet.utils.exploration.flux_analysis) (in module padmet.utils.exploration.get_pwy_from_rxn) (in module padmet.utils.exploration.padmet_stats) (in module padmet.utils.exploration.prot2genome) (in module padmet.utils.exploration.report_network) (in module padmet.utils.exploration.visu_network) (in module padmet.utils.exploration.visu_path) (in module padmet.utils.exploration.visu_similarity_gsmn) (in module padmet.utils.gbr) (in module padmet.utils.management.manual_curation) (in module padmet.utils.management.padmet_compart) (in module padmet.utils.management.padmet_medium) (in module padmet.utils.management.relation_curation)

compare() (padmet.classes.relation.Relation method) compare_multiple_sbml() (in module padmet.utils.exploration.compare_sbml) compare_padmet() (in module padmet.utils.exploration.compare_padmet) compare_padmet_cli() (in module padmet.utils.exploration.compare_padmet) compare_rxn() (in module padmet.utils.exploration.compare_sbml) compare_sbml() (in module padmet.utils.exploration.compare_sbml) compare_sbml_cli() (in module padmet.utils.exploration.compare_sbml) compare_sbml_padmet() (in module padmet.utils.exploration.compare_sbml_padmet) compare_sbml_padmet_cli() (in module padmet.utils.exploration.compare_sbml_padmet) comparison_cluster() (in module padmet.utils.exploration.dendrogram_reactions_distance) compile_input() (in module padmet.utils.gbr) compound_to_sbml() (in module padmet.utils.connection.sbmlGenerator) compounds_parser() (in module padmet.utils.connection.pgdb_to_padmet) compute_stats() (in module padmet.utils.exploration.padmet_stats) convert_from_coded_id() (in module padmet.utils.sbmlPlugin) convert_sbml_db_cli() (in module padmet.utils.exploration.convert_sbml_db) convert_to_coded_id() (in module padmet.utils.sbmlPlugin) copy_io_files() (in module padmet.utils.connection.wikiGenerator) copyNode() (padmet.classes.padmetSpec.PadmetSpec method) create_annotation() (in module padmet.utils.connection.sbmlGenerator) create_biological_page() (in module padmet.utils.connection.wikiGenerator) create_cluster() (in module padmet.utils.exploration.dendrogram_reactions_distance) create_graph() (in module padmet.utils.exploration.visu_network) create_html_graph() (in module padmet.utils.exploration.visu_network) create_intersection_files() (in module padmet.utils.exploration.dendrogram_reactions_distance) create_intervene_graph() (in module padmet.utils.exploration.dendrogram_reactions_distance) create_json_from_padmet() (in module padmet.utils.connection.metexploreviz_export) create_json_from_sbml() (in module padmet.utils.connection.metexploreviz_export) create_log_page() (in module padmet.utils.connection.wikiGenerator) create_main() (in module padmet.utils.connection.wikiGenerator) create_navigation_page() (in module padmet.utils.connection.wikiGenerator) create_note() (in module padmet.utils.connection.sbmlGenerator) create_prot_ids_fasta() (in module padmet.utils.connection.pgdb_to_padmet) create_pvclust_dendrogram() (in module padmet.utils.exploration.dendrogram_reactions_distance) create_supervenn() (in module padmet.utils.exploration.dendrogram_reactions_distance) create_venn() (in module padmet.utils.connection.wikiGenerator) createDirectory() (in module padmet.utils.connection.wikiGenerator) createNode() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) createPadmet() (in module padmet.utils.exploration.prot2genome) createSeqFromTblastn() (in module padmet.utils.exploration.prot2genome)

D

delCompart() (padmet.classes.padmetSpec.PadmetSpec method) delNode() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) dendrogram_reactions_distance_cli() (in module padmet.utils.exploration.dendrogram_reactions_distance)

dict_data_to_sbml() (in module padmet.utils.connection.extract_orthofinder) dict_pwys_to_file() (in module padmet.utils.exploration.get_pwy_from_rxn) draw_ellipse() (in module padmet.utils.connection.wikiGenerator) draw_text() (in module padmet.utils.connection.wikiGenerator)

E

EndOfFile (padmet.utils.gbr.Type attribute) enhance_db() (in module padmet.utils.connection.pgdb_to_padmet) enhanced_meneco_output() (in module padmet.utils.connection.enhanced_meneco_output) enhanced_meneco_output_cli() (in module padmet.utils.connection.enhanced_meneco_output) entity_xref_file() (in module padmet.utils.connection.padmet_to_tsv) enzrxns_parser() (in module padmet.utils.connection.pgdb_to_padmet) Error (class in padmet.utils.gbr) eval_tree() (in module padmet.utils.gbr) extract_element_ontology() (in module padmet.utils.connection.get_metacyc_ontology) extract_entity_xref() (in module padmet.utils.connection.padmet_to_tsv) extract_information_padmet() (in module padmet.utils.exploration.compare_padmet) extract_nodes() (in module padmet.utils.connection.padmet_to_tsv) extract_orthofinder_cli() (in module padmet.utils.connection.extract_orthofinder) extract_padmet_data() (in module padmet.utils.connection.wikiGenerator)

extract_pathway() (padmet.classes.padmetSpec.PadmetSpec method) extract_prot_ids() (in module padmet.utils.connection.pgdb_to_padmet) extract_pwy() (in module padmet.utils.connection.padmet_to_tsv) extract_pwys() (in module padmet.utils.exploration.get_pwy_from_rxn) extract_rxn_cpd() (in module padmet.utils.connection.padmet_to_tsv) extract_rxn_gene() (in module padmet.utils.connection.padmet_to_tsv) extract_rxn_pwy() (in module padmet.utils.connection.padmet_to_tsv) extract_rxn_rec() (in module padmet.utils.connection.padmet_to_tsv) extract_rxn_with_gene_assoc() (in module padmet.utils.connection.extract_rxn_with_gene_assoc) extract_rxn_with_gene_assoc_cli() (in module padmet.utils.connection.extract_rxn_with_gene_assoc) extract_sequence() (in module padmet.utils.exploration.prot2genome) extractAnalysis() (in module padmet.utils.exploration.prot2genome) extractFormula() (in module padmet.utils.sbmlPlugin) extractGenes() (in module padmet.utils.exploration.prot2genome) extractReactions() (in module padmet.utils.exploration.prot2genome)

F

fba_on_targets() (in module padmet.utils.exploration.flux_analysis) Finish (padmet.utils.gbr.Command attribute) flux_analysis() (in module padmet.utils.exploration.flux_analysis) flux_analysis_cli() (in module padmet.utils.exploration.flux_analysis)

from_init_source() (in module padmet.utils.connection.sbmlGenerator) from_pgdb_to_padmet() (in module padmet.utils.connection.pgdb_to_padmet) from_sbml_to_sbml() (in module padmet.utils.connection.sbml_to_sbml) fromAucome() (in module padmet.utils.exploration.prot2genome)

G

gbk_to_faa() (in module padmet.utils.connection.gbk_to_faa) gbk_to_faa_cli() (in module padmet.utils.connection.gbk_to_faa) gbr_cli() (in module padmet.utils.gbr) gene_to_targets() (in module padmet.utils.connection.gene_to_targets) gene_to_targets_cli() (in module padmet.utils.connection.gene_to_targets) generate_fsm() (in module padmet.utils.gbr) generate_syntree() (in module padmet.utils.gbr) generateFile() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) genes_parser() (in module padmet.utils.connection.pgdb_to_padmet) get_all_compart() (padmet.classes.padmetSpec.PadmetSpec method) get_all_decoded_version() (in module padmet.utils.sbmlPlugin) get_cmd_label() (in module padmet.utils.connection.wikiGenerator) get_from_mnx() (in module padmet.utils.exploration.convert_sbml_db) get_growth_medium() (padmet.classes.padmetSpec.PadmetSpec method) get_labels() (in module padmet.utils.connection.wikiGenerator) get_metacyc_ontology_cli() (in module padmet.utils.connection.get_metacyc_ontology) get_pwy_from_rxn() (in module padmet.utils.exploration.get_pwy_from_rxn) get_pwy_from_rxn_cli() (in module padmet.utils.exploration.get_pwy_from_rxn) get_relations() (in module padmet.utils.management.relation_curation)

get_sbml_files() (in module padmet.utils.connection.extract_orthofinder) get_valid_faa() (in module padmet.utils.connection.check_orthology_input) getAllRelation() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) getClassOfNode() (padmet.classes.policy.Policy method) getCompounds() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) getGenes() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) getNewick() (in module padmet.utils.exploration.dendrogram_reactions_distance) getPathways() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) getPathwaysReactions() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) getPolicyInArray() (padmet.classes.policy.Policy method) getReactions() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) getRelation() (padmet.classes.padmetSpec.PadmetSpec method) getRelationTypeIDIn() (padmet.classes.padmetSpec.PadmetSpec method) getTypeOfArc() (padmet.classes.policy.Policy method)

H

hclust_to_xml() (in module padmet.utils.exploration.dendrogram_reactions_distance)

I

instantiate_padmet() (in module padmet.classes.instantiation)

intern_mapping() (in module padmet.utils.exploration.convert_sbml_db)

K

ko() (padmet.classes.padmetSpec.PadmetSpec method)

L

Letter (padmet.utils.gbr.Type attribute) lexical_analysis() (in module padmet.utils.gbr)

loadGraph() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method)

M

manage_medium() (in module padmet.utils.management.padmet_medium) manual_curation_cli() (in module padmet.utils.management.manual_curation) map_gene_id() (in module padmet.utils.connection.pgdb_to_padmet) map_sbml() (in module padmet.utils.exploration.convert_sbml_db) merge_dicts() (in module padmet.utils.exploration.compare_padmet) metacyc_to_ontology() (in module padmet.utils.connection.get_metacyc_ontology) metexploreviz_export() (in module padmet.utils.connection.metexploreviz_export) metexploreviz_export_cli() (in module padmet.utils.connection.metexploreviz_export) mnx_reader() (in module padmet.utils.exploration.convert_sbml_db) modelSeed_to_padmet() (in module padmet.utils.connection.modelSeed_to_padmet) modelSeed_to_padmet_cli() (in module padmet.utils.connection.modelSeed_to_padmet) module padmet.classes.instantiation padmet.classes.node padmet.classes.padmetRef padmet.classes.padmetSpec padmet.classes.policy padmet.classes.relation padmet.utils.connection.biggAPI_to_padmet padmet.utils.connection.check_orthology_input padmet.utils.connection.enhanced_meneco_output padmet.utils.connection.extract_orthofinder padmet.utils.connection.extract_rxn_with_gene_assoc padmet.utils.connection.gbk_to_faa padmet.utils.connection.gene_to_targets padmet.utils.connection.get_metacyc_ontology padmet.utils.connection.metexploreviz_export padmet.utils.connection.modelSeed_to_padmet padmet.utils.connection.padmet_to_asp padmet.utils.connection.padmet_to_matrix padmet.utils.connection.padmet_to_padmet padmet.utils.connection.padmet_to_tsv padmet.utils.connection.pgdb_to_padmet padmet.utils.connection.sbml_to_curation_form padmet.utils.connection.sbml_to_padmet padmet.utils.connection.sbml_to_sbml padmet.utils.connection.sbmlGenerator padmet.utils.connection.wikiGenerator padmet.utils.exploration.compare_padmet padmet.utils.exploration.compare_sbml padmet.utils.exploration.compare_sbml_padmet padmet.utils.exploration.convert_sbml_db padmet.utils.exploration.dendrogram_reactions_distance padmet.utils.exploration.flux_analysis padmet.utils.exploration.get_pwy_from_rxn padmet.utils.exploration.padmet_stats padmet.utils.exploration.prot2genome padmet.utils.exploration.report_network padmet.utils.exploration.visu_network padmet.utils.exploration.visu_path padmet.utils.exploration.visu_similarity_gsmn padmet.utils.gbr padmet.utils.management.manual_curation padmet.utils.management.padmet_compart padmet.utils.management.padmet_medium padmet.utils.management.relation_curation padmet.utils.sbmlPlugin

mp_createPadmet() (in module padmet.utils.exploration.prot2genome) mp_extractReactions() (in module padmet.utils.exploration.prot2genome) mp_runAnalysis() (in module padmet.utils.exploration.prot2genome)

N

network_report() (padmet.classes.padmetSpec.PadmetSpec method)

Node (class in padmet.classes.node)

O

ontology_to_newick() (in module padmet.utils.connection.get_metacyc_ontology) Op (padmet.utils.gbr.Type attribute) Opening (padmet.utils.gbr.Type attribute)

orthogroups_to_sbml() (in module padmet.utils.connection.extract_orthofinder) orthologue_to_sbml() (in module padmet.utils.connection.extract_orthofinder) orthology_result() (in module padmet.utils.exploration.padmet_stats) Other (padmet.utils.gbr.Type attribute)

P

padmet.classes.instantiation module padmet.classes.node module padmet.classes.padmetRef module padmet.classes.padmetSpec module padmet.classes.policy module padmet.classes.relation module padmet.utils.connection.biggAPI_to_padmet module padmet.utils.connection.check_orthology_input module padmet.utils.connection.enhanced_meneco_output module padmet.utils.connection.extract_orthofinder module padmet.utils.connection.extract_rxn_with_gene_assoc module padmet.utils.connection.gbk_to_faa module padmet.utils.connection.gene_to_targets module padmet.utils.connection.get_metacyc_ontology module padmet.utils.connection.metexploreviz_export module padmet.utils.connection.modelSeed_to_padmet module padmet.utils.connection.padmet_to_asp module padmet.utils.connection.padmet_to_matrix module padmet.utils.connection.padmet_to_padmet module padmet.utils.connection.padmet_to_tsv module padmet.utils.connection.pgdb_to_padmet module padmet.utils.connection.sbml_to_curation_form module padmet.utils.connection.sbml_to_padmet module padmet.utils.connection.sbml_to_sbml module padmet.utils.connection.sbmlGenerator module padmet.utils.connection.wikiGenerator module padmet.utils.exploration.compare_padmet module padmet.utils.exploration.compare_sbml module padmet.utils.exploration.compare_sbml_padmet module padmet.utils.exploration.convert_sbml_db module padmet.utils.exploration.dendrogram_reactions_distance module

padmet.utils.exploration.flux_analysis module padmet.utils.exploration.get_pwy_from_rxn module padmet.utils.exploration.padmet_stats module padmet.utils.exploration.prot2genome module padmet.utils.exploration.report_network module padmet.utils.exploration.visu_network module padmet.utils.exploration.visu_path module padmet.utils.exploration.visu_similarity_gsmn module padmet.utils.gbr module padmet.utils.management.manual_curation module padmet.utils.management.padmet_compart module padmet.utils.management.padmet_medium module padmet.utils.management.relation_curation module padmet.utils.sbmlPlugin module padmet_compart_cli() (in module padmet.utils.management.padmet_compart) padmet_medium_cli() (in module padmet.utils.management.padmet_medium) padmet_stat() (in module padmet.utils.exploration.padmet_stats) padmet_stats_cli() (in module padmet.utils.exploration.padmet_stats) padmet_to_asp() (in module padmet.utils.connection.padmet_to_asp) padmet_to_asp_cli() (in module padmet.utils.connection.padmet_to_asp) padmet_to_matrix() (in module padmet.utils.connection.padmet_to_matrix) padmet_to_matrix_cli() (in module padmet.utils.connection.padmet_to_matrix) padmet_to_padmet() (in module padmet.utils.connection.padmet_to_padmet) padmet_to_padmet_cli() (in module padmet.utils.connection.padmet_to_padmet) padmet_to_sbml() (in module padmet.utils.connection.sbmlGenerator) padmet_to_tsv() (in module padmet.utils.connection.padmet_to_tsv) padmet_to_tsv_cli() (in module padmet.utils.connection.padmet_to_tsv) PadmetRef (class in padmet.classes.padmetRef) PadmetSpec (class in padmet.classes.padmetSpec) parse_compounds_padmet() (in module padmet.utils.exploration.visu_network) parse_compounds_sbml() (in module padmet.utils.exploration.visu_network) parse_mnx_chem_prop() (in module padmet.utils.connection.sbmlGenerator) parse_mnx_chem_xref() (in module padmet.utils.connection.sbmlGenerator) parse_pathways_padmet() (in module padmet.utils.exploration.visu_network) parse_reactions_padmet() (in module padmet.utils.exploration.visu_network) parseGeneAssoc() (in module padmet.utils.sbmlPlugin) parseNotes() (in module padmet.utils.sbmlPlugin) pathways_parser() (in module padmet.utils.connection.pgdb_to_padmet) pgdb_to_padmet_cli() (in module padmet.utils.connection.pgdb_to_padmet) Policy (class in padmet.classes.policy) postfix() (in module padmet.utils.gbr) precedence() (in module padmet.utils.gbr) prefix() (in module padmet.utils.gbr) prot2genome_cli() (in module padmet.utils.exploration.prot2genome) proteins_parser() (in module padmet.utils.connection.pgdb_to_padmet) proteins_seq_ids_reduced_70_dat_parser() (in module padmet.utils.connection.pgdb_to_padmet) pvclust_dendrogram() (in module padmet.utils.exploration.dendrogram_reactions_distance) pwy_rate() (in module padmet.utils.connection.padmet_to_tsv)

R

reaction_figure_creation() (in module padmet.utils.exploration.dendrogram_reactions_distance) reaction_to_sbml() (in module padmet.utils.connection.sbmlGenerator) reactions_parser() (in module padmet.utils.connection.pgdb_to_padmet) reduce_padmet_data() (in module padmet.utils.connection.wikiGenerator) Relation (class in padmet.classes.relation) relation_curation_cli() (in module padmet.utils.management.relation_curation) remove_compart() (in module padmet.utils.management.padmet_compart) remove_growth_medium() (padmet.classes.padmetSpec.PadmetSpec method) replace_compart() (in module padmet.utils.management.padmet_compart) report_network_cli() (in module padmet.utils.exploration.report_network) rnas_parser() (in module padmet.utils.connection.pgdb_to_padmet)

run_sbml_to_sbml() (in module padmet.utils.connection.sbml_to_sbml) runAllAnalysis() (in module padmet.utils.exploration.prot2genome) runBlastp() (in module padmet.utils.exploration.prot2genome) runExonerate() (in module padmet.utils.exploration.prot2genome) runSearchOnProteome() (in module padmet.utils.exploration.prot2genome) runTblastn() (in module padmet.utils.exploration.prot2genome) rxn_cpd_file() (in module padmet.utils.connection.padmet_to_tsv) rxn_creator() (in module padmet.utils.management.manual_curation) rxn_gene_file() (in module padmet.utils.connection.padmet_to_tsv) rxn_pwy_file() (in module padmet.utils.connection.padmet_to_tsv) rxn_rec_file() (in module padmet.utils.connection.padmet_to_tsv)

S

sbml_to_curation() (in module padmet.utils.connection.sbml_to_curation_form) sbml_to_curation_form_cli() (in module padmet.utils.connection.sbml_to_curation_form) sbml_to_padmet() (in module padmet.utils.connection.sbml_to_sbml) sbml_to_padmet_cli() (in module padmet.utils.connection.sbml_to_padmet) sbml_to_padmetRef() (in module padmet.utils.connection.sbml_to_padmet) sbml_to_padmetSpec() (in module padmet.utils.connection.sbml_to_padmet) sbml_to_sbml_cli() (in module padmet.utils.connection.sbml_to_sbml) sbmlGenerator_cli() (in module padmet.utils.connection.sbmlGenerator) select_nodes_links() (in module padmet.utils.connection.metexploreviz_export) set_growth_medium() (padmet.classes.padmetSpec.PadmetSpec method) setDicOfNode() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method)

setdicOfRelationIn() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) setdicOfRelationOut() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) setInfo() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) setPolicy() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) setPolicyInArray() (padmet.classes.policy.Policy method) sniff_datafile() (in module padmet.utils.management.manual_curation) Stack (padmet.utils.gbr.Command attribute)

T

template_add_delete() (in module padmet.utils.management.manual_curation) template_new_rxn() (in module padmet.utils.management.manual_curation) toString() (padmet.classes.node.Node method) (padmet.classes.relation.Relation method)

Type (class in padmet.utils.gbr) type_of() (in module padmet.utils.gbr)

U

UnexpectedChar (padmet.utils.gbr.Error attribute) UnexpectedClosing (padmet.utils.gbr.Error attribute) UnexpectedLetter (padmet.utils.gbr.Error attribute) UnexpectedOp (padmet.utils.gbr.Error attribute) UnexpectedOpening (padmet.utils.gbr.Error attribute)

update_basic_attrib() (in module padmet.utils.connection.wikiGenerator) updateFromPadmet() (padmet.classes.padmetSpec.PadmetSpec method) updateFromSbml() (padmet.classes.padmetRef.PadmetRef method) (padmet.classes.padmetSpec.PadmetSpec method) updateNode() (padmet.classes.padmetSpec.PadmetSpec method)

V

venn4() (in module padmet.utils.connection.wikiGenerator) visu_network_cli() (in module padmet.utils.exploration.visu_network) visu_path_cli() (in module padmet.utils.exploration.visu_path)

visu_path_compounds() (in module padmet.utils.exploration.visu_path) visu_path_pathways() (in module padmet.utils.exploration.visu_path) visu_similarity_gsmn() (in module padmet.utils.exploration.visu_similarity_gsmn) visu_similarity_gsmn_cli() (in module padmet.utils.exploration.visu_similarity_gsmn)

W

well_parenthesed() (in module padmet.utils.gbr)

wikiGenerator() (in module padmet.utils.connection.wikiGenerator) wikiGenerator_cli() (in module padmet.utils.connection.wikiGenerator)

X

xrefLink() (in module padmet.utils.connection.wikiGenerator)