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API documentation for padmet.classes
API documentation for padmet.utils
Connection
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Management
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Index
A
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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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H
|
I
|
K
|
L
|
M
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N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
|
X
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_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.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.sbmlGenerator)
(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.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)
,
[1]
(in module padmet.utils.exploration.padmet_stats)
(in module padmet.utils.exploration.prot2genome)
(in module padmet.utils.exploration.visu_path)
(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_intersection_files() (in module padmet.utils.exploration.dendrogram_reactions_distance)
create_intervene_graph() (in module padmet.utils.exploration.dendrogram_reactions_distance)
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_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)
,
[1]
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_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_pwy() (in module padmet.utils.connection.padmet_to_tsv)
extract_pwys() (in module padmet.utils.exploration.get_pwy_from_rxn)
,
[1]
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_pwy_from_rxn() (in module padmet.utils.exploration.get_pwy_from_rxn)
,
[1]
get_pwy_from_rxn_cli() (in module padmet.utils.exploration.get_pwy_from_rxn)
,
[1]
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)
getNewick() (in module padmet.utils.exploration.dendrogram_reactions_distance)
getPolicyInArray() (padmet.classes.policy.Policy 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
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)
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)
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
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.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.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)
,
[1]
padmet.utils.exploration.padmet_stats (module)
padmet.utils.exploration.prot2genome (module)
padmet.utils.exploration.visu_path (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_mnx_chem_prop() (in module padmet.utils.connection.sbmlGenerator)
parse_mnx_chem_xref() (in module padmet.utils.connection.sbmlGenerator)
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)
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)
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)
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_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)
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)
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