v1.0.0
Table of content
1. Functions
2. Requirements
3. Installation
4. Test case
5. API
CobraMod
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Index
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Index
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B
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C
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D
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F
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G
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J
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K
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M
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N
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P
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R
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S
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T
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U
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V
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W
A
AbbreviationWarning
add_marker() (cobramod.visualization.converter.JsonDictionary method)
add_members() (cobramod.core.pathway.Pathway method)
(cobramod.Pathway method)
add_metabolite() (cobramod.visualization.converter.JsonDictionary method)
(cobramod.visualization.items.Reaction method)
add_metabolites() (in module cobramod)
(in module cobramod.core.creation)
add_pathway() (in module cobramod)
(in module cobramod.core.extension)
add_reaction() (cobramod.visualization.converter.JsonDictionary method)
add_reactions() (in module cobramod)
(in module cobramod.core.creation)
add_segment() (cobramod.visualization.items.Reaction method)
add_segments() (cobramod.visualization.converter.JsonDictionary method)
available_databases (in module cobramod)
(in module cobramod.core.retrieval)
B
back() (in module cobramod.core.graph)
BaseParser (class in cobramod.parsing)
(class in cobramod.parsing.base)
BiggParser (class in cobramod.parsing)
(class in cobramod.parsing.bigg)
BiocycParser (class in cobramod.parsing)
(class in cobramod.parsing.biocyc)
build_graph() (in module cobramod.core.graph)
C
CANVAS_HEIGHT (cobramod.visualization.converter.JsonDictionary attribute)
CANVAS_WIDTH (cobramod.visualization.converter.JsonDictionary attribute)
check_imbalance() (in module cobramod.utils)
child_map() (in module cobramod.visualization.mapping)
cobra_tolerance (in module cobramod.core.extension)
cobramod
module
cobramod.core
module
cobramod.core.creation
module
cobramod.core.extension
module
cobramod.core.genes
module
cobramod.core.graph
module
cobramod.core.pathway
module
cobramod.core.retrieval
module
cobramod.core.summary
module
cobramod.debug
module
cobramod.error
module
cobramod.parsing
module
cobramod.parsing.base
module
cobramod.parsing.bigg
module
cobramod.parsing.biocyc
module
cobramod.parsing.kegg
module
cobramod.parsing.plantcyc
module
cobramod.test
module
cobramod.utils
module
cobramod.visualization
module
cobramod.visualization.converter
module
cobramod.visualization.debug
module
cobramod.visualization.items
module
cobramod.visualization.mapping
module
cobramod.visualization.pair
module
color_grading() (cobramod.visualization.converter.JsonDictionary method)
compare_DictList() (in module cobramod.utils)
compare_type() (in module cobramod.utils)
create_object() (in module cobramod)
(in module cobramod.core.creation)
create_replacement() (in module cobramod.utils)
cut_cycle() (in module cobramod.core.graph)
cut_parents() (in module cobramod.core.graph)
D
data_dir (in module cobramod.test)
Databases (class in cobramod.core.retrieval)
databases (in module cobramod.parsing.biocyc)
DataModel (class in cobramod.core.summary)
debug_formatter (in module cobramod.debug)
(in module cobramod.visualization.debug)
debug_handler (in module cobramod.debug)
(in module cobramod.visualization.debug)
debug_log (in module cobramod.debug)
(in module cobramod.visualization.debug)
diff() (cobramod.core.summary.DataModel method)
F
fill_matrix() (in module cobramod.visualization.mapping)
find_cycle() (in module cobramod.core.graph)
find_missing() (in module cobramod.core.graph)
format_matrix() (in module cobramod.visualization.mapping)
FoundInPairError
from_model() (cobramod.core.summary.DataModel class method)
G
get_all_values() (in module cobramod.visualization.mapping)
get_canvas() (cobramod.visualization.converter.JsonDictionary method)
get_data() (in module cobramod)
(in module cobramod.core.retrieval)
get_graph() (in module cobramod.parsing.biocyc)
(in module cobramod.parsing.kegg)
(in module cobramod.parsing.plantcyc)
get_index() (in module cobramod.visualization.mapping)
get_key_dict() (in module cobramod.utils)
get_mapping() (in module cobramod.core.graph)
(in module cobramod.visualization.mapping)
get_paths() (in module cobramod.core.graph)
GraphKeyError
J
json_dump() (cobramod.visualization.converter.JsonDictionary method)
JsonDictionary (class in cobramod.visualization.converter)
K
KeggParser (class in cobramod.parsing)
(class in cobramod.parsing.kegg)
M
map_metabolites() (cobramod.visualization.converter.JsonDictionary method)
marker() (cobramod.visualization.items.Node method)
metabolite() (cobramod.visualization.items.Node method)
model_convert() (in module cobramod)
(in module cobramod.core.pathway)
modify_graph() (cobramod.core.pathway.Pathway method)
(cobramod.Pathway method)
module
cobramod
cobramod.core
cobramod.core.creation
cobramod.core.extension
cobramod.core.genes
cobramod.core.graph
cobramod.core.pathway
cobramod.core.retrieval
cobramod.core.summary
cobramod.debug
cobramod.error
cobramod.parsing
cobramod.parsing.base
cobramod.parsing.bigg
cobramod.parsing.biocyc
cobramod.parsing.kegg
cobramod.parsing.plantcyc
cobramod.test
cobramod.utils
cobramod.visualization
cobramod.visualization.converter
cobramod.visualization.debug
cobramod.visualization.items
cobramod.visualization.mapping
cobramod.visualization.pair
N
Node (class in cobramod.visualization.items)
NodeAttributeError
NoDelimiter
NoGeneInformation
NoIntersectFound
NotInRangeError
P
PairDictionary (class in cobramod.visualization.pair)
parsers (in module cobramod.core.retrieval)
Pathway (class in cobramod)
(class in cobramod.core.pathway)
PatternNotFound
PlantCycParser (class in cobramod.parsing)
(class in cobramod.parsing.plantcyc)
Position (in module cobramod.visualization.converter)
R
R_HEIGHT (cobramod.visualization.converter.JsonDictionary attribute)
R_WIDTH (cobramod.visualization.converter.JsonDictionary attribute)
Reaction (class in cobramod.visualization.items)
reaction_data (cobramod.visualization.converter.JsonDictionary attribute)
response (in module cobramod.parsing.biocyc)
retrieve_data() (in module cobramod.parsing.bigg)
(in module cobramod.parsing.biocyc)
(in module cobramod.parsing.kegg)
(in module cobramod.parsing.plantcyc)
return_cycles() (in module cobramod.core.graph)
S
Segment (class in cobramod.visualization.items)
set_pair() (cobramod.visualization.pair.PairDictionary method)
solution() (cobramod.core.pathway.Pathway method)
(cobramod.Pathway method)
summary() (in module cobramod.core.summary)
SuperpathwayWarning
T
test_non_zero_flux() (in module cobramod)
(in module cobramod.core.extension)
textbook (in module cobramod.test)
textbook_biocyc (in module cobramod.test)
textbook_kegg (in module cobramod.test)
to_csv() (cobramod.core.summary.DataModel method)
to_excl() (cobramod.core.summary.DataModel method)
to_txt() (cobramod.core.summary.DataModel method)
translate() (in module cobramod)
(in module cobramod.core.retrieval)
transpose() (in module cobramod.visualization.mapping)
U
UnbalancedReaction
unformatted_matrix() (in module cobramod.visualization.mapping)
V
verify_paths() (in module cobramod.core.graph)
visualize() (cobramod.core.pathway.Pathway method)
(cobramod.Pathway method)
(cobramod.visualization.converter.JsonDictionary method)
W
write_to_file() (in module cobramod.utils)
WrongDataError
WrongParserError
WrongSyntax
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