FEV@KEGG
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FEV@KEGG
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__eq__() (FEV_KEGG.Graph.Models.CommonGraphApi method)
__initBulk__() (FEV_KEGG.KEGG.Organism.Organism class method)
__ne__() (FEV_KEGG.Graph.Models.CommonGraphApi method)
__str__() (FEV_KEGG.KEGG.SSDB.JSONpickable method)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry method)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway method)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction method)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Relation method)
_as_string() (in module FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
_as_unicode() (in module FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
_binary_to_string_handle() (in module FEV_KEGG.lib.Biopython.KEGG.REST)
_filterGlobalAndOverview() (FEV_KEGG.KEGG.Organism.Organism class method)
_filterHomologsBySignificanceBulk() (in module FEV_KEGG.KEGG.Database)
_filterNonMetabolic() (FEV_KEGG.KEGG.Organism.Organism method)
_getGraphsParallelly() (FEV_KEGG.KEGG.Organism.Group method)
_is_int_or_long() (in module FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
_SubstanceReactionGraph2SubstanceEcGraph() (FEV_KEGG.KEGG.NUKA.NUKA method)
A
add_component() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry method)
add_entry() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway method)
add_graphics() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry method)
add_product() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction method)
add_reaction() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway method)
add_relation() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway method)
add_substrate() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction method)
addColourAttribute() (in module FEV_KEGG.Drawing.Export)
addDescription() (FEV_KEGG.Graph.Elements.EcNumber method)
addDescriptionAttribute() (in module FEV_KEGG.Drawing.Export)
addEC() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
addEcDescriptions() (FEV_KEGG.Graph.Elements.EcNumber static method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
addEdge() (FEV_KEGG.Graph.Models.CommonGraphApi method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
addEdges() (FEV_KEGG.Graph.Models.CommonGraphApi method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
addedMetabolism() (FEV_KEGG.Evolution.Clade.CladePair method)
addedMetabolismEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
addedMetabolismGeneDuplicatedEnzymePairs() (FEV_KEGG.Evolution.Clade.CladePair method)
addedMetabolismGeneDuplicatedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
addedMetabolismNeofunctionalisedECs() (FEV_KEGG.Evolution.Clade.CladePair method)
addedMetabolismNeofunctionalisedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
addEnzyme() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
addGene() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
addIdAttribute() (in module FEV_KEGG.Drawing.Export)
addLabelAttribute() (in module FEV_KEGG.Drawing.Export)
addMajorityAttribute() (in module FEV_KEGG.Drawing.Export)
addNode() (FEV_KEGG.Graph.Models.CommonGraphApi method)
addNodes() (FEV_KEGG.Graph.Models.CommonGraphApi method)
addReaction() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceReactionGraph method)
addReactionAttribute() (in module FEV_KEGG.Drawing.Export)
addSubstanceDescriptions() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGraph method)
addUrlAttribute() (in module FEV_KEGG.Drawing.Export)
archaea (FEV_KEGG.Evolution.LUCA.CoreLUCA.CladeType attribute)
archaeaBacteria (FEV_KEGG.Evolution.LUCA.CoreLUCA.CladeType attribute)
archaeaEukaryota (FEV_KEGG.Evolution.LUCA.CoreLUCA.CladeType attribute)
atomic_write() (in module FEV_KEGG.KEGG.File)
automaticallyStartProcessPool (in module FEV_KEGG.settings)
B
bacteria (FEV_KEGG.Evolution.LUCA.CoreLUCA.CladeType attribute)
bacteriaEukaryota (FEV_KEGG.Evolution.LUCA.CoreLUCA.CladeType attribute)
bgcolor (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
BLUE (FEV_KEGG.Drawing.Export.Colour attribute)
bounds (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
C
cache() (in module FEV_KEGG.KEGG.File)
CacheEntry (class in FEV_KEGG.KEGG.File)
cacheEntry() (in module FEV_KEGG.KEGG.File)
cachePath (in module FEV_KEGG.settings)
centre (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
ChevronGeneDuplication (class in FEV_KEGG.Evolution.Events)
childNCBInames (FEV_KEGG.Evolution.Clade.CladePair attribute)
chunks() (in module FEV_KEGG.Util.Util)
Clade (class in FEV_KEGG.Evolution.Clade)
CladePair (class in FEV_KEGG.Evolution.Clade)
collectiveEcGraph() (FEV_KEGG.KEGG.Organism.Group method)
collectiveEnzymeGraph() (FEV_KEGG.KEGG.Organism.Group method)
collectiveEnzymeGraphByEcConsensus() (FEV_KEGG.KEGG.Organism.Group method)
collectiveEnzymeGraphByEcMajority() (FEV_KEGG.KEGG.Organism.Group method)
collectiveMetabolism() (FEV_KEGG.Evolution.Clade.Clade method)
(FEV_KEGG.Evolution.LUCA.CoreLUCA method)
collectiveMetabolismEnzymes() (FEV_KEGG.Evolution.Clade.Clade method)
Colour (class in FEV_KEGG.Drawing.Export)
COLOUR_NAME (in module FEV_KEGG.Drawing.Export)
colourGraph() (FEV_KEGG.Evolution.Events.NeofunctionalisedECs method)
(FEV_KEGG.Evolution.Events.NeofunctionalisedEnzymes method)
CommonGraphApi (class in FEV_KEGG.Graph.Models)
Comparison (class in FEV_KEGG.Robustness.Topology.Redundancy)
Component (class in FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
composeAll() (FEV_KEGG.Graph.Models.CommonGraphApi class method)
compounds (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
consensusEcGraph() (FEV_KEGG.KEGG.Organism.Group method)
conservedMetabolism() (FEV_KEGG.Evolution.Clade.CladePair method)
conservedMetabolismEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
conservedMetabolismGeneDuplicatedEnzymePairs() (FEV_KEGG.Evolution.Clade.CladePair method)
conservedMetabolismGeneDuplicatedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
conservedMetabolismNeofunctionalisedECs() (FEV_KEGG.Evolution.Clade.CladePair method)
conservedMetabolismNeofunctionalisedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
contains() (FEV_KEGG.Graph.Elements.EcNumber method)
ContributionComparison (class in FEV_KEGG.Robustness.Topology.Redundancy)
Conversion (class in FEV_KEGG.Graph.SubstanceGraphs)
coords (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
copy() (FEV_KEGG.Graph.Models.CommonGraphApi method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceReactionGraph method)
CoreLUCA (class in FEV_KEGG.Evolution.LUCA)
CoreLUCA.CladeType (class in FEV_KEGG.Evolution.LUCA)
coreMetabolism() (FEV_KEGG.Evolution.Clade.Clade method)
(FEV_KEGG.Evolution.LUCA.CoreLUCA method)
coreMetabolismEnzymes() (FEV_KEGG.Evolution.Clade.Clade method)
createPath() (in module FEV_KEGG.KEGG.File)
D
deduplicateList() (in module FEV_KEGG.Util.Util)
default (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
defaultEValue (in module FEV_KEGG.Evolution.Clade)
(in module FEV_KEGG.Evolution.Events)
defaultEvalue (in module FEV_KEGG.settings)
defaultExcludeMultifunctionalEnzymes (in module FEV_KEGG.Evolution.Clade)
defaultExcludeUnclassified (in module FEV_KEGG.Evolution.Clade)
defaultMajorityPercentageCoreMetabolism (in module FEV_KEGG.Evolution.Clade)
defaultMajorityPercentageNeofunctionalisation (in module FEV_KEGG.Evolution.Clade)
defaultNoMultifunctional (in module FEV_KEGG.settings)
defaultOneOrganismPerSpecies (in module FEV_KEGG.Evolution.Clade)
(in module FEV_KEGG.settings)
DESCRIPTION_NAME (in module FEV_KEGG.Drawing.Export)
dictToHtml() (in module FEV_KEGG.Util.Util)
dictToHtmlFile() (in module FEV_KEGG.Util.Util)
difference() (FEV_KEGG.Graph.Models.CommonGraphApi method)
DirectedMultiGraph (class in FEV_KEGG.Graph.Models)
divergedMetabolism() (FEV_KEGG.Evolution.Clade.CladePair method)
divergedMetabolismEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
divergedMetabolismGeneDuplicatedEnzymePairs() (FEV_KEGG.Evolution.Clade.CladePair method)
divergedMetabolismGeneDuplicatedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
divergedMetabolismNeofunctionalisedECs() (FEV_KEGG.Evolution.Clade.CladePair method)
divergedMetabolismNeofunctionalisedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
doesFileExist() (in module FEV_KEGG.KEGG.File)
doesFolderExist() (in module FEV_KEGG.KEGG.File)
doesOrganismExist() (in module FEV_KEGG.KEGG.Database)
doesOrganismExistBulk() (in module FEV_KEGG.KEGG.Database)
downloadEcEnzyme() (in module FEV_KEGG.KEGG.Download)
downloadEnzymeEcNumbers() (in module FEV_KEGG.KEGG.Download)
downloadGene() (in module FEV_KEGG.KEGG.Download)
downloadGeneBulk() (in module FEV_KEGG.KEGG.Download)
downloadOrganismInfo() (in module FEV_KEGG.KEGG.Download)
downloadOrganismList() (in module FEV_KEGG.KEGG.Download)
downloadOrthologOverview() (in module FEV_KEGG.KEGG.Download)
downloadOrthologs() (in module FEV_KEGG.KEGG.Download)
downloadParalogs() (in module FEV_KEGG.KEGG.Download)
downloadPathway() (in module FEV_KEGG.KEGG.Download)
downloadPathwayList() (in module FEV_KEGG.KEGG.Download)
downloadSubstance() (in module FEV_KEGG.KEGG.Download)
downloadTaxonomyKEGG() (in module FEV_KEGG.KEGG.Download)
downloadTaxonomyNCBI() (in module FEV_KEGG.KEGG.Download)
downloadThreads (in module FEV_KEGG.settings)
downloadThreadsPerProcess (in module FEV_KEGG.settings)
downloadThreadsPerProcessSSDB (in module FEV_KEGG.settings)
downloadThreadsSSDB (in module FEV_KEGG.settings)
downloadTimeout (in module FEV_KEGG.settings)
downloadTimeoutSocket (in module FEV_KEGG.settings)
DrugIdError
E
ecCounts (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph attribute)
EcEnzyme (class in FEV_KEGG.KEGG.DataTypes)
ecGraphs() (FEV_KEGG.KEGG.Organism.Group method)
EcNumber (class in FEV_KEGG.Graph.Elements)
ecNumberLevelsInteger (FEV_KEGG.Graph.Elements.EcNumber attribute)
ecNumbers (FEV_KEGG.Evolution.LUCA.GoldmanLUCA attribute)
edges (FEV_KEGG.Graph.Models.MutablePath attribute)
(FEV_KEGG.Graph.Models.Path attribute)
edgesExpanded (FEV_KEGG.Graph.Models.MutablePath attribute)
(FEV_KEGG.Graph.Models.Path attribute)
Element (class in FEV_KEGG.Graph.Elements)
element (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Component attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Relation attribute)
elongate() (FEV_KEGG.Graph.Models.MutablePath method)
enableShallCancelThreads() (in module FEV_KEGG.Util.Parallelism)
enterobacterialesEcGraph() (in module FEV_KEGG.Experiments.19)
(in module FEV_KEGG.Experiments.20)
enterobacterialesEcSets() (in module FEV_KEGG.Experiments.22)
Entry (class in FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
entry (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction attribute)
entry1 (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Relation attribute)
entry2 (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Relation attribute)
Enzyme (class in FEV_KEGG.Graph.Elements)
EnzymeComplete (class in FEV_KEGG.Graph.Elements)
enzymeCounts (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph attribute)
enzymeGraphs() (FEV_KEGG.KEGG.Organism.Group method)
eukaryota (FEV_KEGG.Evolution.LUCA.CoreLUCA.CladeType attribute)
F
FEV_KEGG (module)
FEV_KEGG.Drawing (module)
FEV_KEGG.Drawing.Draw (module)
FEV_KEGG.Drawing.Export (module)
FEV_KEGG.Evolution (module)
FEV_KEGG.Evolution.Clade (module)
FEV_KEGG.Evolution.Comparison (module)
FEV_KEGG.Evolution.Events (module)
FEV_KEGG.Evolution.LUCA (module)
FEV_KEGG.Evolution.Taxonomy (module)
FEV_KEGG.Experiments (module)
FEV_KEGG.Experiments.01 (module)
FEV_KEGG.Experiments.02 (module)
FEV_KEGG.Experiments.03 (module)
FEV_KEGG.Experiments.04 (module)
FEV_KEGG.Experiments.05 (module)
FEV_KEGG.Experiments.06 (module)
FEV_KEGG.Experiments.07 (module)
FEV_KEGG.Experiments.08 (module)
FEV_KEGG.Experiments.09 (module)
FEV_KEGG.Experiments.10 (module)
FEV_KEGG.Experiments.11 (module)
FEV_KEGG.Experiments.12 (module)
FEV_KEGG.Experiments.13 (module)
FEV_KEGG.Experiments.14 (module)
FEV_KEGG.Experiments.15 (module)
FEV_KEGG.Experiments.16 (module)
FEV_KEGG.Experiments.17 (module)
FEV_KEGG.Experiments.18 (module)
FEV_KEGG.Experiments.19 (module)
FEV_KEGG.Experiments.20 (module)
FEV_KEGG.Experiments.21 (module)
FEV_KEGG.Experiments.22 (module)
FEV_KEGG.Experiments.23 (module)
FEV_KEGG.Experiments.24 (module)
FEV_KEGG.Experiments.25 (module)
FEV_KEGG.Experiments.26 (module)
FEV_KEGG.Experiments.27 (module)
FEV_KEGG.Experiments.28 (module)
FEV_KEGG.Experiments.29 (module)
FEV_KEGG.Experiments.30 (module)
FEV_KEGG.Experiments.31 (module)
FEV_KEGG.Experiments.32 (module)
FEV_KEGG.Experiments.33 (module)
FEV_KEGG.Experiments.34 (module)
FEV_KEGG.Experiments.35 (module)
FEV_KEGG.Experiments.36 (module)
FEV_KEGG.Experiments.37 (module)
FEV_KEGG.Experiments.38 (module)
FEV_KEGG.Experiments.39 (module)
FEV_KEGG.Experiments.40 (module)
FEV_KEGG.Experiments.41 (module)
FEV_KEGG.Experiments.42 (module)
FEV_KEGG.Experiments.43 (module)
FEV_KEGG.Experiments.44 (module)
FEV_KEGG.Experiments.45 (module)
FEV_KEGG.Experiments.46 (module)
FEV_KEGG.Experiments.47 (module)
FEV_KEGG.Experiments.48 (module)
FEV_KEGG.Experiments.49 (module)
FEV_KEGG.Experiments.50 (module)
FEV_KEGG.Experiments.51 (module)
FEV_KEGG.Experiments.52 (module)
FEV_KEGG.Experiments.53 (module)
FEV_KEGG.Experiments.54 (module)
FEV_KEGG.Experiments.55 (module)
FEV_KEGG.Graph (module)
FEV_KEGG.Graph.Elements (module)
FEV_KEGG.Graph.Implementations (module)
FEV_KEGG.Graph.Implementations.NetworkX (module)
FEV_KEGG.Graph.Models (module)
FEV_KEGG.Graph.SubstanceGraphs (module)
FEV_KEGG.KEGG (module)
FEV_KEGG.KEGG.Database (module)
FEV_KEGG.KEGG.DataTypes (module)
FEV_KEGG.KEGG.Download (module)
FEV_KEGG.KEGG.File (module)
FEV_KEGG.KEGG.NUKA (module)
FEV_KEGG.KEGG.Organism (module)
FEV_KEGG.KEGG.SSDB (module)
FEV_KEGG.lib (module)
FEV_KEGG.lib.Biopython (module)
FEV_KEGG.lib.Biopython.KEGG (module)
FEV_KEGG.lib.Biopython.KEGG.KGML (module)
FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_parser (module)
FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway (module)
FEV_KEGG.lib.Biopython.KEGG.REST (module)
FEV_KEGG.lib.Python (module)
FEV_KEGG.lib.Python.concurrent (module)
FEV_KEGG.lib.Python.concurrent.futures (module)
FEV_KEGG.quirks (module)
FEV_KEGG.Robustness (module)
FEV_KEGG.Robustness.Topology (module)
FEV_KEGG.Robustness.Topology.Redundancy (module)
FEV_KEGG.Robustness.Topology.Statistics (module)
FEV_KEGG.settings (module)
FEV_KEGG.Statistics (module)
FEV_KEGG.Statistics.Percent (module)
FEV_KEGG.Statistics.SequenceComparison (module)
FEV_KEGG.UnitTest (module)
FEV_KEGG.UnitTest.collectiveEnzymeGraphByEcConsensus (module)
FEV_KEGG.UnitTest.collectiveEnzymeGraphByEcMajority (module)
FEV_KEGG.Util (module)
FEV_KEGG.Util.Parallelism (module)
FEV_KEGG.Util.Util (module)
fgcolor (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
fileThreads (in module FEV_KEGG.settings)
fileThreadsPerProcess (in module FEV_KEGG.settings)
filterEnzymes() (FEV_KEGG.Evolution.Events.ChevronGeneDuplication method)
(FEV_KEGG.Evolution.Events.SimpleGeneDuplication class method)
(FEV_KEGG.Evolution.Events.SimpleGroupGeneDuplication method)
filterGraph() (FEV_KEGG.Evolution.Events.NeofunctionalisedECs method)
(FEV_KEGG.Evolution.Events.NeofunctionalisedEnzymes method)
Flexibility (class in FEV_KEGG.Robustness.Topology.Redundancy)
FLEXIBILITY (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
FLEXIBILITY_BOTH (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
FLEXIBILITY_PARTIAL (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
FlexibilityContribution (class in FEV_KEGG.Robustness.Topology.Redundancy)
floatToPercentString() (in module FEV_KEGG.Statistics.Percent)
forCytoscape() (in module FEV_KEGG.Drawing.Export)
freeHeap() (FEV_KEGG.KEGG.Organism.Group method)
fromArray() (FEV_KEGG.Graph.Elements.EcNumber class method)
fromClade() (FEV_KEGG.Robustness.Topology.Redundancy.Robustness class method)
fromCladePair() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison class method)
fromDirectedMultiGraph() (FEV_KEGG.Graph.Models.UndirectedMultiGraph class method)
fromGene() (FEV_KEGG.Graph.Elements.Enzyme class method)
fromGraph() (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyContribution class method)
fromMatch() (FEV_KEGG.KEGG.SSDB.TransientMatch class method)
fromNeofunctionalisation() (FEV_KEGG.Evolution.Events.FunctionChange class method)
fromOrganismGroup() (FEV_KEGG.Robustness.Topology.Redundancy.Robustness class method)
fromOrganismGroups() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison class method)
fromPathway() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceReactionGraph static method)
fromPreMatch() (FEV_KEGG.KEGG.SSDB.Match class method)
fromSubstanceEnzymeGraph() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph static method)
fromSubstanceGeneGraph() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph static method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph static method)
fromSubstanceReactionGraph() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph static method)
fruchterman_reingold() (FEV_KEGG.Drawing.Draw.NetworkxLayout method)
FunctionChange (class in FEV_KEGG.Evolution.Events)
G
gammaproteobacteriaEcGraph() (in module FEV_KEGG.Experiments.19)
(in module FEV_KEGG.Experiments.20)
gammaproteobacteriaEcSets() (in module FEV_KEGG.Experiments.22)
Gene (class in FEV_KEGG.KEGG.DataTypes)
geneCounts (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph attribute)
GeneDoesNotExistError
geneDuplicatedEnzymePairs() (FEV_KEGG.Evolution.Clade.Clade method)
geneDuplicatedEnzymes() (FEV_KEGG.Evolution.Clade.Clade method)
geneDuplicatedEnzymesDict() (FEV_KEGG.Evolution.Clade.Clade method)
GeneDuplication (class in FEV_KEGG.Evolution.Events)
GeneFunctionAddition (class in FEV_KEGG.Evolution.Events)
GeneFunctionConservation (class in FEV_KEGG.Evolution.Events)
GeneFunctionDivergence (class in FEV_KEGG.Evolution.Events)
GeneFunctionLoss (class in FEV_KEGG.Evolution.Events)
GeneID (class in FEV_KEGG.Graph.Elements)
geneName (FEV_KEGG.Graph.Elements.GeneID attribute)
genes (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
get_KGML() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway method)
getAddedRedundancyKeyContributionRatio() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getAddedRedundancyKeys() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getAddedRedundancyKeysPathsForKey() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getAddedRedundancyPaths() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getAddedRedundancyRatio() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getArchaeaClade() (in module FEV_KEGG.Experiments.40)
(in module FEV_KEGG.Experiments.41)
(in module FEV_KEGG.Experiments.42)
getBacteriaClade() (in module FEV_KEGG.Experiments.41)
getClade() (in module FEV_KEGG.Experiments.45)
(in module FEV_KEGG.Experiments.51)
(in module FEV_KEGG.Experiments.54)
(in module FEV_KEGG.Experiments.55)
getCladeA() (in module FEV_KEGG.Experiments.44)
(in module FEV_KEGG.Experiments.46)
(in module FEV_KEGG.Experiments.47)
(in module FEV_KEGG.Experiments.48)
(in module FEV_KEGG.Experiments.49)
(in module FEV_KEGG.Experiments.50)
(in module FEV_KEGG.Experiments.52)
(in module FEV_KEGG.Experiments.53)
getCladeB() (in module FEV_KEGG.Experiments.44)
(in module FEV_KEGG.Experiments.50)
getComponents() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getConservedRedundancyKeyContributionRatio() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getConservedRedundancyKeys() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getConservedRedundancyKeysPathsForKey() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getConservedRedundancyPaths() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getConservedRedundancyRatio() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getContributedAddedRedundancyKeysForSpecial() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedAddedRedundancyPaths() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedAddedRedundancyPathsForKey() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedConservedRedundancyKeysForSpecial() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedConservedRedundancyPaths() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedConservedRedundancyPathsForKey() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedKeysForSpecial() (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyContribution method)
getContributedLostRedundancyKeysForSpecial() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedLostRedundancyPaths() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedLostRedundancyPathsForKey() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getContributedPaths() (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyContribution method)
getContributedPathsForKey() (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyContribution method)
getContributingSpecialForKey() (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyContribution method)
getDesulfobacteralesClade() (in module FEV_KEGG.Experiments.43)
getDifferingEcLevels() (FEV_KEGG.Evolution.Events.FunctionChange method)
(FEV_KEGG.Evolution.Events.Neofunctionalisation method)
getEcEnzymeBulk() (in module FEV_KEGG.KEGG.Database)
getEcNumbers() (FEV_KEGG.Evolution.Events.Neofunctionalisation method)
getEcNumbersString() (FEV_KEGG.Graph.Elements.Enzyme method)
getECs() (FEV_KEGG.Evolution.Events.GeneFunctionAddition static method)
(FEV_KEGG.Evolution.Events.GeneFunctionConservation static method)
(FEV_KEGG.Evolution.Events.GeneFunctionDivergence static method)
(FEV_KEGG.Evolution.Events.GeneFunctionLoss static method)
(FEV_KEGG.Evolution.Events.NeofunctionalisedECs method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
getEdgeKeys() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getEdges() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getEdgesForKey() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getEdgesFromKey() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getEnzymeEcNumbers() (in module FEV_KEGG.KEGG.Database)
getEnzymeForGeneID() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
getEnzymePairs() (FEV_KEGG.Evolution.Events.ChevronGeneDuplication method)
(FEV_KEGG.Evolution.Events.SimpleGeneDuplication class method)
(FEV_KEGG.Evolution.Events.SimpleGroupGeneDuplication method)
getEnzymes() (FEV_KEGG.Evolution.Events.ChevronGeneDuplication method)
(FEV_KEGG.Evolution.Events.Neofunctionalisation method)
(FEV_KEGG.Evolution.Events.NeofunctionalisedEnzymes method)
(FEV_KEGG.Evolution.Events.SimpleGeneDuplication static method)
(FEV_KEGG.Evolution.Events.SimpleGroupGeneDuplication method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
getEnzymesForEC() (FEV_KEGG.Evolution.Events.NeofunctionalisedECs method)
getEnzymesForEcNumber() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
getEnzymesForFunctionChange() (FEV_KEGG.Evolution.Events.NeofunctionalisedECs method)
getExpectationValue() (in module FEV_KEGG.Statistics.SequenceComparison)
getFileHandleRead() (in module FEV_KEGG.KEGG.File)
getFileHandleWrite() (in module FEV_KEGG.KEGG.File)
getFunctionChanges() (FEV_KEGG.Evolution.Events.NeofunctionalisedECs method)
getGammaproteobacteriaClade() (in module FEV_KEGG.Experiments.40)
getGene() (FEV_KEGG.KEGG.Organism.Organism method)
(in module FEV_KEGG.KEGG.Database)
getGeneBulk() (in module FEV_KEGG.KEGG.Database)
getGeneByID() (FEV_KEGG.KEGG.Organism.Organism method)
getGeneByName() (FEV_KEGG.KEGG.Organism.Organism method)
getGeneID() (FEV_KEGG.KEGG.DataTypes.Gene method)
getGeneIDs() (FEV_KEGG.KEGG.Organism.Organism method)
getGeneIDsByName() (FEV_KEGG.KEGG.Organism.Organism method)
getGeneIDsByPathway() (FEV_KEGG.KEGG.Organism.Organism method)
getGeneIDsForEcNumber() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
getGenes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
(FEV_KEGG.KEGG.Organism.Organism method)
getGenesByName() (FEV_KEGG.KEGG.Organism.Organism method)
getGenesByPathway() (FEV_KEGG.KEGG.Organism.Organism method)
getGraph() (FEV_KEGG.Evolution.Events.GeneFunctionAddition static method)
(FEV_KEGG.Evolution.Events.GeneFunctionConservation static method)
(FEV_KEGG.Evolution.Events.GeneFunctionDivergence static method)
(FEV_KEGG.Evolution.Events.GeneFunctionLoss static method)
getIsolatedNodes() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getKeyContributionRatio() (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyContribution method)
getLargestComponent() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getLargestComponentNodes() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getLostRedundancyKeyContributionRatio() (FEV_KEGG.Robustness.Topology.Redundancy.ContributionComparison method)
getLostRedundancyKeys() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getLostRedundancyPaths() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getLostRedundancyPathsForKey() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getLostRedundancyRatio() (FEV_KEGG.Robustness.Topology.Redundancy.Comparison method)
getMetabolicPathwayDescriptions() (FEV_KEGG.KEGG.Organism.Organism method)
getMetabolicPathways() (FEV_KEGG.KEGG.Organism.Organism method)
getMultifunctionalEnzymeEdges() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
getMultifunctionalEnzymes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
getMultifunctionalGeneEdges() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
getMultifunctionalGenes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
getNeofunctionalisations() (FEV_KEGG.Evolution.Events.NeofunctionalisedEnzymes method)
getNeofunctionalisationsForEC() (FEV_KEGG.Evolution.Events.NeofunctionalisedECs method)
getNeofunctionalisationsForFunctionChange() (FEV_KEGG.Evolution.Events.NeofunctionalisedECs method)
getNodes() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getNumberOfGenes() (FEV_KEGG.KEGG.Organism.Organism method)
getNumberOfThreadsDownload() (in module FEV_KEGG.Util.Parallelism)
getNumberOfThreadsFile() (in module FEV_KEGG.Util.Parallelism)
getOrganismAbbreviations() (FEV_KEGG.Evolution.Taxonomy.Taxonomy method)
getOrganismAbbreviationsByName() (FEV_KEGG.Evolution.Taxonomy.Taxonomy method)
getOrganismAbbreviationsByPath() (FEV_KEGG.Evolution.Taxonomy.Taxonomy method)
getOrganismInfo() (in module FEV_KEGG.KEGG.Database)
getOrganismList() (in module FEV_KEGG.KEGG.Database)
getOrganismNodeByAbbreviation() (FEV_KEGG.Evolution.Taxonomy.Taxonomy method)
getOrganismNodesByName() (FEV_KEGG.Evolution.Taxonomy.Taxonomy method)
getOrganismNodesByPath() (FEV_KEGG.Evolution.Taxonomy.Taxonomy method)
getOrthologOverviewsBulk() (in module FEV_KEGG.KEGG.Database)
getOrthologs() (in module FEV_KEGG.KEGG.Database)
getOrthologsBulk() (in module FEV_KEGG.KEGG.Database)
getOrthologsOnlyGeneID() (in module FEV_KEGG.KEGG.Database)
getOrthologsWithinEnzymes() (in module FEV_KEGG.Evolution.Comparison)
getOrthologsWithinGeneIDs() (in module FEV_KEGG.Evolution.Comparison)
getParalogs() (in module FEV_KEGG.KEGG.Database)
getParalogsBulk() (in module FEV_KEGG.KEGG.Database)
getParalogsOnlyGeneID() (in module FEV_KEGG.KEGG.Database)
getPartialEcNumberEdges() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
getPartialEcNumbers() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
getPaths() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getPathway() (FEV_KEGG.KEGG.Organism.Organism method)
(in module FEV_KEGG.KEGG.Database)
getPathwayBulk() (in module FEV_KEGG.KEGG.Database)
getPathwayDescriptions() (FEV_KEGG.KEGG.Organism.Organism method)
(in module FEV_KEGG.KEGG.Database)
getPathwayGeneIDs() (in module FEV_KEGG.KEGG.Database)
getPathwayIDs() (FEV_KEGG.KEGG.Organism.Organism method)
getPathwayNames() (FEV_KEGG.KEGG.Organism.Organism method)
getPathways() (FEV_KEGG.KEGG.Organism.Organism method)
getPathwaysFromNames() (FEV_KEGG.KEGG.Organism.Organism method)
getPercent() (in module FEV_KEGG.Statistics.Percent)
getPercentSentence() (in module FEV_KEGG.Statistics.Percent)
getPercentString() (in module FEV_KEGG.Statistics.Percent)
getPercentStringShort() (in module FEV_KEGG.Statistics.Percent)
getReactions() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceReactionGraph method)
getRedundancyPaths() (FEV_KEGG.Robustness.Topology.Redundancy.Redundancy method)
getRedundancyPathsForKey() (FEV_KEGG.Robustness.Topology.Redundancy.Redundancy method)
getRedundancyRatio() (FEV_KEGG.Robustness.Topology.Redundancy.Redundancy method)
getRedundantKeys() (FEV_KEGG.Robustness.Topology.Redundancy.Redundancy method)
getRestUrl() (FEV_KEGG.Graph.Elements.Element method)
getResult() (FEV_KEGG.KEGG.File.CacheEntry method)
getShallCancelThreads() (in module FEV_KEGG.Util.Parallelism)
getShortestPaths() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getSubgraph() (FEV_KEGG.Graph.Models.CommonGraphApi method)
getSubstanceBulk() (in module FEV_KEGG.KEGG.Database)
getTaxonomy() (FEV_KEGG.Evolution.Taxonomy.KEGG static method)
(FEV_KEGG.Evolution.Taxonomy.NCBI static method)
getTaxonomyKEGG() (in module FEV_KEGG.KEGG.Database)
getTaxonomyNCBI() (in module FEV_KEGG.KEGG.Database)
getTqdmPosition() (in module FEV_KEGG.Util.Parallelism)
getTransientMatches() (FEV_KEGG.KEGG.SSDB.MatchingOverview method)
getUnidirectionalEcNumbers() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
getUnidirectionalEdges() (FEV_KEGG.Graph.Models.DirectedMultiGraph method)
getUnidirectionalEdgesElements() (FEV_KEGG.Graph.Models.DirectedMultiGraph method)
getUnidirectionalEnzymes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
getUnidirectionalGenes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
getUnidirectionalReactions() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceReactionGraph method)
getUrl() (FEV_KEGG.Graph.Elements.Element method)
GLOBAL_PATHWAY_PATTERN (FEV_KEGG.KEGG.Organism.Organism attribute)
GoldmanLUCA (class in FEV_KEGG.Evolution.LUCA)
Graphics (class in FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
GREEN (FEV_KEGG.Drawing.Export.Colour attribute)
Group (class in FEV_KEGG.KEGG.Organism)
groupEcGraph() (in module FEV_KEGG.Experiments.23)
(in module FEV_KEGG.Experiments.25)
H
hasOrthologsBulk() (in module FEV_KEGG.KEGG.Database)
hasSpecialKey (FEV_KEGG.Graph.Models.MarkedPath attribute)
hasSpecialNode (FEV_KEGG.Graph.Models.MarkedPath attribute)
hasWildcard() (FEV_KEGG.Graph.Elements.EcNumber method)
height (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
I
id (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Component attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction attribute)
ID_NAME (in module FEV_KEGG.Drawing.Export)
implementationGraph (FEV_KEGG.Graph.Models.DirectedMultiGraph attribute)
(FEV_KEGG.Graph.Models.UndirectedMultiGraph attribute)
implementationLib (FEV_KEGG.Graph.Models.CommonGraphApi attribute)
ImpossiblyOrthologousError
insertWildcards() (FEV_KEGG.Graph.Elements.EcNumber static method)
InterruptibleProcessPoolExecutor (class in FEV_KEGG.lib.Python.concurrent.futures)
intersection() (FEV_KEGG.Graph.Models.CommonGraphApi method)
inverseDictKeepingAllKeys() (in module FEV_KEGG.Util.Util)
is_not_404() (in module FEV_KEGG.KEGG.Download)
is_reactant (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry attribute)
isKnownToKEGG() (in module FEV_KEGG.Experiments.33)
isMainProcess() (in module FEV_KEGG.Util.Parallelism)
isMainThread() (in module FEV_KEGG.Util.Parallelism)
isMainThreadInMainProcess() (in module FEV_KEGG.Util.Parallelism)
isMatchSignificant() (in module FEV_KEGG.Statistics.SequenceComparison)
isSameEcReaction() (FEV_KEGG.Evolution.Events.Neofunctionalisation method)
J
JSONpickable (class in FEV_KEGG.KEGG.SSDB)
K
kamada_kawai() (FEV_KEGG.Drawing.Draw.NetworkxLayout method)
keepEnzymesByEC() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
KEGG (class in FEV_KEGG.Evolution.Taxonomy)
kegg_conv() (in module FEV_KEGG.lib.Biopython.KEGG.REST)
kegg_find() (in module FEV_KEGG.lib.Biopython.KEGG.REST)
kegg_get() (in module FEV_KEGG.lib.Biopython.KEGG.REST)
kegg_info() (in module FEV_KEGG.lib.Biopython.KEGG.REST)
kegg_link() (in module FEV_KEGG.lib.Biopython.KEGG.REST)
kegg_list() (in module FEV_KEGG.lib.Biopython.KEGG.REST)
KeggOrthologyID (class in FEV_KEGG.Graph.Elements)
KeggPathway2SubstanceReactionGraph() (FEV_KEGG.Graph.SubstanceGraphs.Conversion static method)
KeggPathwaySet2SubstanceReactionGraph() (FEV_KEGG.Graph.SubstanceGraphs.Conversion class method)
keyboardInterruptHandler() (in module FEV_KEGG.Util.Parallelism)
KGMLParser (class in FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_parser)
L
LABEL_NAME (in module FEV_KEGG.Drawing.Export)
lostMetabolism() (FEV_KEGG.Evolution.Clade.CladePair method)
lostMetabolismEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
lostMetabolismGeneDuplicatedEnzymePairs() (FEV_KEGG.Evolution.Clade.CladePair method)
lostMetabolismGeneDuplicatedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
lostMetabolismNeofunctionalisedECs() (FEV_KEGG.Evolution.Clade.CladePair method)
lostMetabolismNeofunctionalisedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
M
MAJORITY_NAME (in module FEV_KEGG.Drawing.Export)
majorityEcGraph() (FEV_KEGG.KEGG.Organism.Group method)
majorityIntersection() (FEV_KEGG.Graph.Models.CommonGraphApi method)
maps (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
MarkedPath (class in FEV_KEGG.Graph.Models)
Match (class in FEV_KEGG.KEGG.SSDB)
Matching (class in FEV_KEGG.KEGG.SSDB)
matchingLevels() (FEV_KEGG.Graph.Elements.EcNumber method)
MatchingOverview (class in FEV_KEGG.KEGG.SSDB)
METABOLIC_PATHWAYS (in module FEV_KEGG.quirks)
metabolicPathways (FEV_KEGG.KEGG.Organism.Organism attribute)
MultiDiGraph (class in FEV_KEGG.Graph.Implementations.NetworkX)
MultiGraph (class in FEV_KEGG.Graph.Implementations.NetworkX)
MutablePath (class in FEV_KEGG.Graph.Models)
N
name (FEV_KEGG.Graph.Models.CommonGraphApi attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
(FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction attribute)
NCBI (class in FEV_KEGG.Evolution.Taxonomy)
Neofunctionalisation (class in FEV_KEGG.Evolution.Events)
neofunctionalisations() (FEV_KEGG.Evolution.Clade.Clade method)
neofunctionalisationsForFunctionChange() (FEV_KEGG.Evolution.Clade.Clade method)
NeofunctionalisedECs (class in FEV_KEGG.Evolution.Events)
neofunctionalisedECs() (FEV_KEGG.Evolution.Clade.Clade method)
NeofunctionalisedEnzymes (class in FEV_KEGG.Evolution.Events)
neofunctionalisedEnzymes() (FEV_KEGG.Evolution.Clade.Clade method)
NestedCladePair (class in FEV_KEGG.Evolution.Clade)
NetworkX (class in FEV_KEGG.Graph.Implementations.NetworkX)
NetworkxLayout (class in FEV_KEGG.Drawing.Draw)
nodePath2String() (FEV_KEGG.Evolution.Taxonomy.Taxonomy static method)
nodes (FEV_KEGG.Graph.Models.MutablePath attribute)
(FEV_KEGG.Graph.Models.Path attribute)
NoKnownPathwaysError
NON_EXISTING_ORGANISMS (in module FEV_KEGG.quirks)
NUKA (class in FEV_KEGG.KEGG.NUKA)
number (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
O
Organism (class in FEV_KEGG.KEGG.Organism)
ORGANISM (FEV_KEGG.Evolution.Taxonomy.TaxonType attribute)
organismAbbreviation (FEV_KEGG.Graph.Elements.GeneID attribute)
organismInfoExpiration (in module FEV_KEGG.settings)
organisms (FEV_KEGG.KEGG.Organism.Group attribute)
organismsCount (FEV_KEGG.Evolution.Clade.Clade attribute)
(FEV_KEGG.KEGG.Organism.Group attribute)
orthologs (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
OTHER (FEV_KEGG.Evolution.Taxonomy.TaxonType attribute)
P
parentNCBInames (FEV_KEGG.Evolution.Clade.CladePair attribute)
parse() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_parser.KGMLParser method)
(in module FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_parser)
partiallyRedundantKeyPaths (FEV_KEGG.Robustness.Topology.Redundancy.Flexibility attribute)
(FEV_KEGG.Robustness.Topology.Redundancy.Robustness attribute)
partiallyRedundantKeys (FEV_KEGG.Robustness.Topology.Redundancy.Robustness attribute)
partiallySourceRedundantKeyPaths (FEV_KEGG.Robustness.Topology.Redundancy.Flexibility attribute)
partiallyTargetRedundantKeyPaths (FEV_KEGG.Robustness.Topology.Redundancy.Flexibility attribute)
Path (class in FEV_KEGG.Graph.Models)
paths (FEV_KEGG.Robustness.Topology.Redundancy.Flexibility attribute)
Pathway (class in FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
PINK (FEV_KEGG.Drawing.Export.Colour attribute)
PreMatch (class in FEV_KEGG.KEGG.SSDB)
prettySortDict() (in module FEV_KEGG.Util.Util)
printBelowProgress() (in module FEV_KEGG.Util.Parallelism)
printElementUrl (in module FEV_KEGG.settings)
process_worker() (in module FEV_KEGG.lib.Python.concurrent.futures)
processes (in module FEV_KEGG.settings)
processPool (in module FEV_KEGG.Util.Parallelism)
products (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction attribute)
R
random() (FEV_KEGG.Drawing.Draw.NetworkxLayout method)
reactant_ids (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction attribute)
Reaction (class in FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
reaction (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry attribute)
reaction_entries (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
REACTION_NAME (in module FEV_KEGG.Drawing.Export)
reactionCounts (FEV_KEGG.Graph.SubstanceGraphs.SubstanceReactionGraph attribute)
ReactionID (class in FEV_KEGG.Graph.Elements)
reactions (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
read() (in module FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_parser)
readBytesFromFileAtOnce() (in module FEV_KEGG.KEGG.File)
readGeneratorFromFileLinewise() (in module FEV_KEGG.KEGG.File)
readListFromFileAtOnce() (in module FEV_KEGG.KEGG.File)
readSetFromFileAtOnce() (in module FEV_KEGG.KEGG.File)
readStringFromFileAtOnce() (in module FEV_KEGG.KEGG.File)
RED (FEV_KEGG.Drawing.Export.Colour attribute)
Redundancy (class in FEV_KEGG.Robustness.Topology.Redundancy)
RedundancyContribution (class in FEV_KEGG.Robustness.Topology.Redundancy)
RedundancyType (class in FEV_KEGG.Robustness.Topology.Redundancy)
redundantECsForContributingNeofunctionalisation() (FEV_KEGG.Evolution.Clade.Clade method)
redundantEdges (FEV_KEGG.Robustness.Topology.Redundancy.Robustness attribute)
redundantKeyPaths (FEV_KEGG.Robustness.Topology.Redundancy.Flexibility attribute)
(FEV_KEGG.Robustness.Topology.Redundancy.Robustness attribute)
redundantKeys (FEV_KEGG.Robustness.Topology.Redundancy.Robustness attribute)
REGEX_PATTERN (FEV_KEGG.Graph.Elements.EcNumber attribute)
(FEV_KEGG.Graph.Elements.GeneID attribute)
(FEV_KEGG.Graph.Elements.KeggOrthologyID attribute)
(FEV_KEGG.Graph.Elements.SubstanceID attribute)
Relation (class in FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway)
relations (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway attribute)
remove_component() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry method)
remove_entry() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway method)
remove_graphics() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Entry method)
remove_reaction() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway method)
remove_relation() (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Pathway method)
removeAllECsExcept() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
removeAllEnzymesExcept() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeAllGenesExcept() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
removeEcEdge() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
removeEcEdges() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
removeECs() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
removeEdge() (FEV_KEGG.Graph.Models.CommonGraphApi method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeEdges() (FEV_KEGG.Graph.Models.CommonGraphApi method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeEdgesByElements() (FEV_KEGG.Graph.Models.CommonGraphApi method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeEnzymeEdge() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeEnzymeEdges() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeEnzymes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeEnzymesByEC() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeGeneEdge() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
removeGeneEdges() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
removeGenes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
removeIsolatedNodes() (FEV_KEGG.Graph.Models.CommonGraphApi method)
removeMultifunctionalEnzymes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
removeMultifunctionalGenes() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph method)
removeNodes() (FEV_KEGG.Graph.Models.CommonGraphApi method)
removePartialEcNumbers() (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph method)
removeSmallComponents() (FEV_KEGG.Graph.Models.CommonGraphApi method)
removeWildcards() (FEV_KEGG.Graph.Elements.EcNumber static method)
replaceEdgeElement() (FEV_KEGG.Graph.Models.CommonGraphApi method)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph method)
replaceNode() (FEV_KEGG.Graph.Models.CommonGraphApi method)
replaceNodes() (FEV_KEGG.Graph.Models.CommonGraphApi method)
resetShallCancelThreads() (in module FEV_KEGG.Util.Parallelism)
retryDownloadBackoffFactor (in module FEV_KEGG.settings)
retryDownloadBackoffMax (in module FEV_KEGG.settings)
retryDownloadMax (in module FEV_KEGG.settings)
Robustness (class in FEV_KEGG.Robustness.Topology.Redundancy)
ROBUSTNESS (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
ROBUSTNESS_BOTH (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
ROBUSTNESS_PARTIAL (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
RobustnessContribution (class in FEV_KEGG.Robustness.Topology.Redundancy)
ROOT (FEV_KEGG.Evolution.Taxonomy.TaxonType attribute)
S
searchNodesByName() (FEV_KEGG.Evolution.Taxonomy.Taxonomy method)
searchNodesByPath() (FEV_KEGG.Evolution.Taxonomy.Taxonomy method)
setPathwayGeneIDs() (in module FEV_KEGG.KEGG.Database)
shallCancelThreads (in module FEV_KEGG.Util.Parallelism)
shell() (FEV_KEGG.Drawing.Draw.NetworkxLayout method)
SimpleGeneDuplication (class in FEV_KEGG.Evolution.Events)
SimpleGroupGeneDuplication (class in FEV_KEGG.Evolution.Events)
SOURCE_FLEXIBILITY (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
SOURCE_FLEXIBILITY_BOTH (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
SOURCE_FLEXIBILITY_PARTIAL (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
sourceRedundantKeyPaths (FEV_KEGG.Robustness.Topology.Redundancy.Flexibility attribute)
SPECIES (FEV_KEGG.Evolution.Taxonomy.TaxonType attribute)
spectral() (FEV_KEGG.Drawing.Draw.NetworkxLayout method)
spring() (FEV_KEGG.Drawing.Draw.NetworkxLayout method)
startProcessPool() (in module FEV_KEGG)
(in module FEV_KEGG.Util.Parallelism)
Substance (class in FEV_KEGG.KEGG.DataTypes)
substanceCounts (FEV_KEGG.Graph.SubstanceGraphs.SubstanceEcGraph attribute)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceEnzymeGraph attribute)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceGeneGraph attribute)
(FEV_KEGG.Graph.SubstanceGraphs.SubstanceReactionGraph attribute)
SubstanceEcGraph (class in FEV_KEGG.Graph.SubstanceGraphs)
substanceEcGraph (FEV_KEGG.Evolution.LUCA.GoldmanLUCA attribute)
(FEV_KEGG.KEGG.NUKA.NUKA attribute)
substanceEcGraph() (FEV_KEGG.KEGG.Organism.Organism method)
SubstanceEnzymeGraph (class in FEV_KEGG.Graph.SubstanceGraphs)
substanceEnzymeGraph() (FEV_KEGG.KEGG.Organism.Organism method)
SubstanceEnzymeGraph2SubstanceEcGraph() (FEV_KEGG.Graph.SubstanceGraphs.Conversion static method)
SubstanceGeneGraph (class in FEV_KEGG.Graph.SubstanceGraphs)
substanceGeneGraph() (FEV_KEGG.KEGG.Organism.Organism method)
SubstanceGeneGraph2SubstanceEcGraph() (FEV_KEGG.Graph.SubstanceGraphs.Conversion static method)
SubstanceGeneGraph2SubstanceEnzymeGraph() (FEV_KEGG.Graph.SubstanceGraphs.Conversion static method)
SubstanceGraph (class in FEV_KEGG.Graph.SubstanceGraphs)
SubstanceID (class in FEV_KEGG.Graph.Elements)
SubstanceReactionGraph (class in FEV_KEGG.Graph.SubstanceGraphs)
substanceReactionGraph (FEV_KEGG.KEGG.NUKA.NUKA attribute)
substanceReactionGraph() (FEV_KEGG.KEGG.Organism.Organism method)
SubstanceReactionGraph2SubstanceGeneGraph() (FEV_KEGG.Graph.SubstanceGraphs.Conversion static method)
substrates (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Reaction attribute)
sumPaths (FEV_KEGG.Robustness.Topology.Redundancy.Flexibility attribute)
supergroupEcGraph() (in module FEV_KEGG.Experiments.23)
(in module FEV_KEGG.Experiments.25)
T
TARGET_FLEXIBILITY (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
TARGET_FLEXIBILITY_BOTH (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
TARGET_FLEXIBILITY_PARTIAL (FEV_KEGG.Robustness.Topology.Redundancy.RedundancyType attribute)
targetRedundantKeyPaths (FEV_KEGG.Robustness.Topology.Redundancy.Flexibility attribute)
Taxonomy (class in FEV_KEGG.Evolution.Taxonomy)
TaxonType (class in FEV_KEGG.Evolution.Taxonomy)
Test (class in FEV_KEGG.UnitTest.collectiveEnzymeGraphByEcConsensus)
(class in FEV_KEGG.UnitTest.collectiveEnzymeGraphByEcMajority)
test_consensusEcGraph_difference() (FEV_KEGG.UnitTest.collectiveEnzymeGraphByEcConsensus.Test method)
test_majorityEcGraph_difference() (FEV_KEGG.UnitTest.collectiveEnzymeGraphByEcMajority.Test method)
toGML() (in module FEV_KEGG.Drawing.Export)
toGraphML() (in module FEV_KEGG.Drawing.Export)
toHtml() (FEV_KEGG.Evolution.Events.FunctionChange method)
(FEV_KEGG.Evolution.Events.Neofunctionalisation method)
(FEV_KEGG.Graph.Elements.Element method)
(FEV_KEGG.Graph.Models.Path method)
toPNG() (in module FEV_KEGG.Drawing.Draw)
toUndirectedGraph() (FEV_KEGG.Graph.Models.DirectedMultiGraph method)
toWindow() (in module FEV_KEGG.Drawing.Draw)
TransientMatch (class in FEV_KEGG.KEGG.SSDB)
TURQUOISE (FEV_KEGG.Drawing.Export.Colour attribute)
U
UndirectedMultiGraph (class in FEV_KEGG.Graph.Models)
unifiedMetabolism() (FEV_KEGG.Evolution.Clade.CladePair method)
unifiedMetabolismEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
unifiedMetabolismGeneDuplicatedEnzymePairs() (FEV_KEGG.Evolution.Clade.CladePair method)
unifiedMetabolismGeneDuplicatedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
unifiedMetabolismNeofunctionalisedECs() (FEV_KEGG.Evolution.Clade.CladePair method)
unifiedMetabolismNeofunctionalisedEnzymes() (FEV_KEGG.Evolution.Clade.CladePair method)
union() (FEV_KEGG.Graph.Models.CommonGraphApi method)
universal (FEV_KEGG.Evolution.LUCA.CoreLUCA.CladeType attribute)
updateDictUpdatingValue() (in module FEV_KEGG.Util.Util)
URL_NAME (in module FEV_KEGG.Drawing.Export)
V
verbosity (in module FEV_KEGG.settings)
W
width (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
WILDCARD (FEV_KEGG.Graph.Elements.EcNumber attribute)
writeToFile() (in module FEV_KEGG.KEGG.File)
writeToFileBytes() (in module FEV_KEGG.KEGG.File)
X
x (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
Y
y (FEV_KEGG.lib.Biopython.KEGG.KGML.KGML_pathway.Graphics attribute)
YELLOW (FEV_KEGG.Drawing.Export.Colour attribute)