MINE-Database
latest
1. Installation
2. Running Pickaxe via Command Line
3. Running Pickaxe
4. Generating Pickaxe Inputs
5. Custom Filters
6. Thermodynamic Calculations
7. API Reference
8. Support
MINE-Database
Index
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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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J
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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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W
A
add_reaction_mass_change() (minedatabase.databases.MINE method)
annotate_peaks() (minedatabase.metabolomics.MetabolomicsDataset method)
assign_ids() (minedatabase.pickaxe.Pickaxe method)
B
BNICE() (in module minedatabase.rules)
build_indexes() (minedatabase.databases.MINE method)
C
c_id (minedatabase.utils.StoichTuple property)
check_product_of_native() (minedatabase.metabolomics.MetabolomicsDataset method)
Chunks (class in minedatabase.utils)
convert_sets_to_lists() (in module minedatabase.utils)
D
dot_product() (in module minedatabase.metabolomics)
E
enumerate_possible_masses() (minedatabase.metabolomics.MetabolomicsDataset method)
establish_db_client() (in module minedatabase.databases)
export_inchi_rxns() (in module minedatabase.compound_io)
export_kbase() (in module minedatabase.compound_io)
export_mol() (in module minedatabase.compound_io)
export_sdf() (in module minedatabase.compound_io)
export_smiles() (in module minedatabase.compound_io)
export_tsv() (in module minedatabase.compound_io)
F
file_to_dict_list() (in module minedatabase.utils)
find_db_hits() (minedatabase.metabolomics.MetabolomicsDataset method)
find_minimal_set() (minedatabase.pickaxe.Pickaxe method)
G
generate_image_files() (minedatabase.databases.MINE method)
get_atom_count() (in module minedatabase.utils)
get_compound_hash() (in module minedatabase.utils)
get_dotted_field() (in module minedatabase.utils)
get_fp() (in module minedatabase.utils)
get_KEGG_comps() (in module minedatabase.metabolomics)
get_reaction_hash() (in module minedatabase.utils)
get_rt() (minedatabase.metabolomics.MetabolomicsDataset method)
get_size() (in module minedatabase.utils)
I
import_mol_dir() (in module minedatabase.compound_io)
import_sdf() (in module minedatabase.compound_io)
import_smiles() (in module minedatabase.compound_io)
J
jaccard() (in module minedatabase.metabolomics)
L
load_compound_set() (minedatabase.pickaxe.Pickaxe method)
load_pickled_pickaxe() (minedatabase.pickaxe.Pickaxe method)
load_targets() (minedatabase.pickaxe.Pickaxe method)
M
MetabolomicsDataset (class in minedatabase.metabolomics)
metacyc_generalized() (in module minedatabase.rules)
metacyc_generalized_as_df() (in module minedatabase.rules)
metacyc_intermediate() (in module minedatabase.rules)
MINE (class in minedatabase.databases)
minedatabase.compound_io
module
minedatabase.databases
module
minedatabase.filters
module
minedatabase.metabolomics
module
minedatabase.pickaxe
module
minedatabase.reactions
module
minedatabase.rules
module
minedatabase.utils
module
module
minedatabase.compound_io
minedatabase.databases
minedatabase.filters
minedatabase.metabolomics
minedatabase.pickaxe
minedatabase.reactions
minedatabase.rules
minedatabase.utils
mongo_ids_to_mine_ids() (in module minedatabase.utils)
ms2_search() (in module minedatabase.metabolomics)
ms_adduct_search() (in module minedatabase.metabolomics)
N
neutralise_charges() (in module minedatabase.utils)
next() (minedatabase.utils.Chunks method)
P
Peak (class in minedatabase.metabolomics)
Pickaxe (class in minedatabase.pickaxe)
pickle_pickaxe() (minedatabase.pickaxe.Pickaxe method)
postsanitize_smiles() (in module minedatabase.utils)
prevent_overwrite() (in module minedatabase.utils)
prune_network() (minedatabase.pickaxe.Pickaxe method)
prune_network_to_targets() (minedatabase.pickaxe.Pickaxe method)
R
read_adduct_names() (in module minedatabase.metabolomics)
read_mgf() (in module minedatabase.metabolomics)
read_msp() (in module minedatabase.metabolomics)
read_mzxml() (in module minedatabase.metabolomics)
S
save_dotted_field() (in module minedatabase.utils)
save_to_mine() (minedatabase.pickaxe.Pickaxe method)
save_to_SBML() (minedatabase.pickaxe.Pickaxe method)
score_compounds() (in module minedatabase.metabolomics)
score_isomers() (minedatabase.metabolomics.Peak method)
spectra_download() (in module minedatabase.metabolomics)
stoich (minedatabase.utils.StoichTuple property)
StoichTuple (class in minedatabase.utils)
Struct (class in minedatabase.metabolomics)
T
transform_all() (minedatabase.pickaxe.Pickaxe method)
transform_all_compounds_with_full() (in module minedatabase.reactions)
W
write_compound_output_file() (minedatabase.pickaxe.Pickaxe method)
write_compounds_to_mine() (in module minedatabase.databases)
write_core_compounds() (in module minedatabase.databases)
write_reaction_output_file() (minedatabase.pickaxe.Pickaxe method)
write_reactions_to_mine() (in module minedatabase.databases)
write_targets_to_mine() (in module minedatabase.databases)
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