metabolike
stable
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metabolike
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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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I
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L
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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
add_kv_to_dict() (in module metabolike.utils)
add_props_to_nodes() (metabolike.db.metacyc.MetacycClient method)
atom_mapping (metabolike.config.MetacycConfig attribute)
available_node_labels (metabolike.db.sbml.SBMLClient attribute)
B
BaseTransformer (class in metabolike.parser.brenda_transformer)
bkms_react_file (metabolike.config.BrendaConfig attribute)
brenda (metabolike.config.Config attribute)
brenda_file (metabolike.config.BrendaConfig attribute)
BrendaConfig (class in metabolike.config)
C
chunk() (in module metabolike.utils)
citation() (metabolike.parser.brenda_transformer.RefTreeTransformer method)
classes (metabolike.config.MetacycConfig attribute)
close() (metabolike.db.neo4j.Neo4jClient method)
collect_atom_mapping_dat_nodes() (metabolike.parser.metacyc.MetacycParser method)
collect_citation_dat_nodes() (metabolike.parser.metacyc.MetacycParser method)
collect_classes_dat_nodes() (metabolike.parser.metacyc.MetacycParser method)
collect_compartments() (metabolike.parser.sbml.SBMLParser static method)
collect_compounds() (metabolike.parser.sbml.SBMLParser method)
collect_compounds_dat_nodes() (metabolike.parser.metacyc.MetacycParser method)
collect_gene_products() (metabolike.parser.sbml.SBMLParser method)
collect_groups() (metabolike.parser.sbml.SBMLParser static method)
collect_pathways_dat_nodes() (metabolike.parser.metacyc.MetacycParser method)
collect_reaction_gene_product_links() (metabolike.parser.sbml.SBMLParser method)
collect_reactions() (metabolike.parser.sbml.SBMLParser method)
collect_reactions_dat_nodes() (metabolike.parser.metacyc.MetacycParser method)
commentary() (metabolike.parser.brenda_transformer.GenericTreeTransformer method)
(metabolike.parser.brenda_transformer.ReactionTreeTransformer method)
CommentaryOnlyTreeTransformer (class in metabolike.parser.brenda_transformer)
compounds (metabolike.config.MetacycConfig attribute)
Config (class in metabolike.config)
content() (metabolike.parser.brenda_transformer.GenericTreeTransformer method)
create() (metabolike.db.neo4j.Neo4jClient method)
create_nodes() (metabolike.db.sbml.SBMLClient method)
D
database (metabolike.config.Neo4jConfig attribute)
(metabolike.db.neo4j.Neo4jClient attribute)
(metabolike.db.sbml.SBMLClient attribute)
db (metabolike.parser.sbml.SBMLParser attribute)
default_cyphers (metabolike.db.sbml.SBMLClient attribute)
description() (metabolike.parser.brenda_transformer.CommentaryOnlyTreeTransformer method)
(metabolike.parser.brenda_transformer.GenericTreeTransformer method)
driver (metabolike.db.neo4j.Neo4jClient attribute)
(metabolike.db.sbml.SBMLClient attribute)
E
entry() (metabolike.parser.brenda_transformer.CommentaryOnlyTreeTransformer method)
(metabolike.parser.brenda_transformer.GenericTreeTransformer method)
(metabolike.parser.brenda_transformer.ReactionTreeTransformer method)
(metabolike.parser.brenda_transformer.RefTreeTransformer method)
F
fix_pathway_nodes() (metabolike.parser.metacyc.MetacycParser method)
G
generate_gene_reaction_rule() (in module metabolike.utils)
GenericTreeTransformer (class in metabolike.parser.brenda_transformer)
get_all_compounds() (metabolike.db.metacyc.MetacycClient method)
get_all_nodes() (metabolike.db.metacyc.MetacycClient method)
get_bkms_tarball() (in module metabolike.parser.bkms_react)
I
input_files (metabolike.parser.metacyc.MetacycParser attribute)
L
load_config() (in module metabolike.config)
M
merge_nodes() (metabolike.db.metacyc.MetacycClient method)
metabolike
module
metabolike.api
module
metabolike.config
module
metabolike.db
module
metabolike.db.metacyc
module
metabolike.db.neo4j
module
metabolike.db.sbml
module
metabolike.main
module
metabolike.parser
module
metabolike.parser.bkms_react
module
metabolike.parser.brenda
module
metabolike.parser.brenda_transformer
module
metabolike.parser.metacyc
module
metabolike.parser.sbml
module
metabolike.utils
module
metacyc (metabolike.config.Config attribute)
metacyc_default_cyphers (metabolike.db.metacyc.MetacycClient attribute)
metacyc_to_graph() (metabolike.db.metacyc.MetacycClient method)
MetacycClient (class in metabolike.db.metacyc)
MetacycConfig (class in metabolike.config)
MetacycParser (class in metabolike.parser.metacyc)
missing_ids (metabolike.parser.metacyc.MetacycParser attribute)
module
metabolike
metabolike.api
metabolike.config
metabolike.db
metabolike.db.metacyc
metabolike.db.neo4j
metabolike.db.sbml
metabolike.main
metabolike.parser
metabolike.parser.bkms_react
metabolike.parser.brenda
metabolike.parser.brenda_transformer
metabolike.parser.metacyc
metabolike.parser.sbml
metabolike.utils
more_commentary() (metabolike.parser.brenda_transformer.ReactionTreeTransformer method)
N
neo4j (metabolike.config.Config attribute)
Neo4jClient (class in metabolike.db.neo4j)
Neo4jConfig (class in metabolike.config)
NUM_ID() (metabolike.parser.brenda_transformer.BaseTransformer method)
P
paper_stat() (metabolike.parser.brenda_transformer.RefTreeTransformer method)
parse_brenda() (in module metabolike.parser.brenda)
password (metabolike.config.Neo4jConfig attribute)
pathways (metabolike.config.MetacycConfig attribute)
protein_id() (metabolike.parser.brenda_transformer.BaseTransformer method)
publications (metabolike.config.MetacycConfig attribute)
pubmed() (metabolike.parser.brenda_transformer.RefTreeTransformer method)
R
reaction() (metabolike.parser.brenda_transformer.ReactionTreeTransformer method)
reactions (metabolike.config.MetacycConfig attribute)
ReactionTreeTransformer (class in metabolike.parser.brenda_transformer)
read() (metabolike.db.neo4j.Neo4jClient method)
read_bkms() (in module metabolike.parser.bkms_react)
read_dat_file() (metabolike.parser.metacyc.MetacycParser static method)
read_sbml() (metabolike.parser.sbml.SBMLParser static method)
read_smiles_dat() (metabolike.parser.metacyc.MetacycParser static method)
read_tx() (metabolike.db.neo4j.Neo4jClient method)
ref_id() (metabolike.parser.brenda_transformer.BaseTransformer method)
(metabolike.parser.brenda_transformer.RefTreeTransformer method)
RefTreeTransformer (class in metabolike.parser.brenda_transformer)
report_missing_ids() (metabolike.parser.metacyc.MetacycParser method)
reversibility() (metabolike.parser.brenda_transformer.ReactionTreeTransformer method)
S
sbml (metabolike.config.MetacycConfig attribute)
sbml_file (metabolike.parser.metacyc.MetacycParser attribute)
(metabolike.parser.sbml.SBMLParser attribute)
sbml_to_graph() (metabolike.db.sbml.SBMLClient method)
SBMLClient (class in metabolike.db.sbml)
SBMLParser (class in metabolike.parser.sbml)
serve() (in module metabolike.main)
setup() (in module metabolike.main)
snake_to_camel() (in module metabolike.utils)
SpecificInfoTreeTransformer (class in metabolike.parser.brenda_transformer)
substrate() (metabolike.parser.brenda_transformer.SpecificInfoTreeTransformer method)
T
TOKEN() (metabolike.parser.brenda_transformer.BaseTransformer method)
U
uri (metabolike.config.Neo4jConfig attribute)
user (metabolike.config.Neo4jConfig attribute)
V
validate_path() (in module metabolike.utils)
W
write() (metabolike.db.neo4j.Neo4jClient method)
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