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RetSynth 2 documentation
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V
A
add2dictionary() (Database.build_MINE_db.BuildMINEdb method)
add_all_info_existing() (Database.build_modelseed.LoadIntoDB method)
add_all_info_new() (Database.build_modelseed.LoadIntoDB method)
add_cluster_info() (Database.build_modelseed.LoadIntoDB method)
add_color() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
add_colortable() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
add_data_2_db() (Database.build_user_rxns_db.AddUserRxns2DB method)
add_external_metabolites() (FBA.optimize_target.OptimizeTarget method)
add_external_reactions() (FBA.optimize_target.OptimizeTarget method)
add_individual_file_info() (in module Database.build_SPRESI_db)
add_info_2_database() (in module Database.build_SPRESI_db)
add_metabolite() (in module Database.build_KEGG_db)
add_metacyc_to_db() (Database.build_metacyc_db.Translate method)
add_model_compounds() (Database.build_modelseed.LoadIntoDB method)
add_model_reactions() (Database.build_modelseed.LoadIntoDB method)
add_product() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
add_products() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
add_reactants() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
(Visualization_graphviz.SP_Graph_dot.GraphDot method)
add_reaction_compound() (Database.build_modelseed.LoadIntoDB method)
add_sink_reaction() (FBA.optimize_target.OptimizeTarget method)
(in module FBA.retrieve_producable_mets)
add_to_preexisting_db() (Database.build_KEGG_db.CompileKEGGIntoDB method)
add_transition() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
addChild() (Visualization_chemdraw.reaction_files.Node method)
AddUserRxns2DB (class in Database.build_user_rxns_db)
alter_name_length() (Visualization_chemdraw.reaction_files.ReactionFiles method)
(Visualization_graphviz.SP_Graph_dot.GraphDot method)
(Visualization_graphviz.reaction_files.ReactionFiles method)
analyze_fluxes() (FBA.compare_results.Compare method)
(FBA.compareKO_results.CompareKO method)
append() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
(Visualization_chemdraw.cdxml_elements.BOX method)
(Visualization_chemdraw.cdxml_elements.COMPOUND method)
(Visualization_chemdraw.cdxml_elements.ELEMENT method)
append_box() (Visualization_chemdraw.cdxml_elements.BOX method)
ARC (class in Visualization_chemdraw.cdxml_elements)
arrays() (Database.build_metacyc_db.MetaCyc method)
ARROW (class in Visualization_chemdraw.cdxml_elements)
B
BOX (class in Visualization_chemdraw.cdxml_elements)
build_atlas() (in module Database.build_ATLAS_db)
build_model() (FBA.build_model.BuildModel method)
build_patric_models() (in module Database.build_modelseed)
BuildKbase() (in module Database.build_kbase_db)
BuildKEGG() (in module Database.build_KEGG_db)
BuildMINEdb (class in Database.build_MINE_db)
BuildModel (class in FBA.build_model)
BuildModelSeed (class in Database.build_modelseed)
C
calculate_tanimoto_score() (Parser.structure_similarity.TanimotoStructureSimilarity method)
CDXML_Editor (class in Visualization_chemdraw.cdxml_editor)
check_cpd_in_db() (Database.build_user_rxns_db.AddUserRxns2DB method)
check_db() (Database.build_metacyc_db.MetaCyc method)
check_reaction_difference() (Database.build_metacyc_db.MetaCyc method)
check_refs() (in module Database.build_SPRESI_db)
Compare (class in FBA.compare_results)
CompareKO (class in FBA.compareKO_results)
CompileKEGGIntoDB (class in Database.build_KEGG_db)
COMPOUND (class in Visualization_chemdraw.cdxml_elements)
compound_translator() (Database.build_metacyc_db.MetaCyc method)
connect_to_database() (Database.query.Connector method)
Connector (class in Database.query)
ConstructInitialLP (class in ShortestPath.constraints)
convert_output_2_xlsx() (Parser.generate_output.Output method)
create_model_tbls() (Database.initialize_database.Createdb method)
Createdb (class in Database.initialize_database)
crop_figure() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
custom_query() (Database.query.Connector method)
cycle_constraints() (ShortestPath.integerprogram_pulp.IntergerProgram method)
cycle_constraints_internal() (ShortestPath.integerprogram_pulp.IntergerProgram method)
D
Database (module)
Database.build_ATLAS_db (module)
Database.build_kbase_db (module)
Database.build_KEGG_db (module)
Database.build_metacyc_db (module)
Database.build_MINE_db (module)
Database.build_modelseed (module)
Database.build_SPRESI_db (module)
Database.build_user_rxns_db (module)
Database.initialize_database (module)
Database.query (module)
Database.remove_duplicate_cpds (module)
dot2graph() (in module Visualization_graphviz.chempyutilgraph_edit)
dump() (Visualization_chemdraw.cdxml_elements.ELEMENT method)
E
ELEMENT (class in Visualization_chemdraw.cdxml_elements)
external_pathanalyze_fluxes() (FBA.compare_results.Compare method)
(FBA.compareKO_results.CompareKO method)
extract_cpd_information() (Database.build_MINE_db.BuildMINEdb method)
extract_db_cpd_ID() (Parser.structure_similarity.TanimotoStructureSimilarity method)
Extract_Information (class in ShortestPath.extractinfo)
extract_KEGG_data() (in module Database.build_ATLAS_db)
(in module Database.build_KEGG_db)
(in module Database.build_kbase_db)
(in module Database.build_metacyc_db)
(in module Database.build_modelseed)
extract_KEGG_orgIDs() (in module Database.build_KEGG_db)
extract_pathwayIDs() (in module Database.build_KEGG_db)
extract_reactionIDs() (in module Database.build_KEGG_db)
extract_source_information() (Database.build_MINE_db.BuildMINEdb method)
extractinfo() (ShortestPath.extractinfo.Extract_Information method)
F
FBA (module)
FBA.build_model (module)
FBA.compare_results (module)
FBA.compareKO_results (module)
FBA.optimize_target (module)
FBA.retrieve_producable_mets (module)
FBA_weights() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
fetching_all_query_results() (in module Database.query)
fetching_one_query_results() (in module Database.query)
file_opener() (Parser.read_targets.Readfile method)
fill_allsolutions() (ShortestPath.integerprogram_pulp.IntergerProgram method)
fill_arrays_4_db() (in module Database.build_ATLAS_db)
fill_compound_arrays() (Database.build_metacyc_db.MetaCyc method)
fill_database() (Database.build_MINE_db.BuildMINEdb method)
(in module Database.build_ATLAS_db)
fill_dictionary() (in module Database.build_ATLAS_db)
fill_dictionary_atlasbiochem() (in module Database.build_ATLAS_db)
fill_final_targets() (Parser.structure_similarity.TanimotoStructureSimilarity method)
fill_new_database() (Database.build_KEGG_db.CompileKEGGIntoDB method)
fill_reaction_components_dict() (Database.build_MINE_db.BuildMINEdb method)
fill_temp_array() (Database.build_metacyc_db.MetaCyc method)
filling_optimal_solution_arrays() (ShortestPath.integerprogram_pulp.IntergerProgram method)
G
generate_cdxml_files() (Visualization_chemdraw.reaction_files.ReactionFiles method)
generate_file() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
generate_flux_legend() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
generate_mol_file() (in module Database.build_SPRESI_db)
generate_output_folders() (Visualization_chemdraw.reaction_files.ReactionFiles method)
(Visualization_graphviz.reaction_files.ReactionFiles method)
generate_reaction_SMILES() (Visualization_graphviz.reaction_files.ReactionFiles method)
generate_reactions() (Database.build_MINE_db.BuildMINEdb method)
generate_sbml_output_folder() (in module Database.build_modelseed)
get_all_compound_keggIDs() (Database.query.Connector method)
get_all_compounds() (Database.query.Connector method)
get_all_cpd_chemicalformulas() (Database.query.Connector method)
get_all_cpd_with_chemicalformula() (Database.query.Connector method)
get_all_cpd_with_search() (Database.query.Connector method)
get_all_fba_models() (Database.query.Connector method)
get_all_keggIDs() (Database.query.Connector method)
get_all_models() (Database.query.Connector method)
get_all_reactions() (Database.query.Connector method)
get_catalysts() (Database.query.Connector method)
get_cdxml() (Visualization_chemdraw.reaction_files.ReactionFiles method)
get_color() (Visualization_chemdraw.cdxml_elements.ELEMENT method)
get_compartment() (Database.query.Connector method)
get_compartment_info() (in module Database.build_kbase_db)
get_complex_reference_details() (in module Database.build_SPRESI_db)
get_compound_compartment() (Database.query.Connector method)
get_compound_ID() (Database.query.Connector method)
get_compound_name() (Database.query.Connector method)
get_compounds_4_rxn() (Database.build_metacyc_db.MetaCyc method)
get_compounds_in_model() (Database.query.Connector method)
get_cpd_casnumber() (Database.query.Connector method)
get_cpd_cdxml() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
get_cpd_chemicalformula() (Database.query.Connector method)
get_data() (in module Database.build_SPRESI_db)
get_db_info() (Parser.read_targets.Readfile method)
get_figure() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
get_flux_differences() (FBA.compare_results.Compare method)
(FBA.compareKO_results.CompareKO method)
get_fp_cf() (Database.build_user_rxns_db.AddUserRxns2DB method)
get_fp_cf_info() (Database.build_metacyc_db.MetaCyc method)
get_genes() (Database.query.Connector method)
get_id() (Visualization_chemdraw.cdxml_elements.ELEMENT method)
get_inchi_4_cpd() (in module Database.build_ATLAS_db)
get_inchi_from_kegg_ID() (in module Database.build_metacyc_db)
get_inchi_values() (in module Database.build_kbase_db)
get_info() (ShortestPath.extractinfo.Extract_Information method)
get_kegg_cpd_ID() (Database.query.Connector method)
get_KEGG_IDs() (in module Database.build_kbase_db)
(in module Database.build_modelseed)
get_kegg_reaction_ID() (Database.query.Connector method)
get_label() (Visualization_chemdraw.cdxml_elements.TEXT method)
get_metabolic_clusters() (in module Database.build_kbase_db)
get_model_from_patric() (Database.build_modelseed.BuildModelSeed method)
get_model_ID() (Database.query.Connector method)
get_model_sorted_cpds() (Database.build_modelseed.LoadIntoDB method)
get_model_sorted_rxns() (Database.build_modelseed.LoadIntoDB method)
get_models_from_cluster() (Database.query.Connector method)
get_mol_from_name() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
get_mol_structure() (in module Database.build_SPRESI_db)
get_organism_ID() (Database.query.Connector method)
get_organism_name() (Database.query.Connector method)
get_original_target() (Parser.structure_similarity.TanimotoStructureSimilarity method)
get_pressure() (Database.query.Connector method)
get_products() (Database.query.Connector method)
get_products_reactions() (Database.query.Connector method)
get_promiscuous_cpds() (Database.build_metacyc_db.MetaCyc method)
get_proteins() (Database.query.Connector method)
get_reactants() (Database.query.Connector method)
get_reactants_reactions() (Database.query.Connector method)
get_reaction_name() (Database.query.Connector method)
get_reaction_species() (Database.query.Connector method)
get_reaction_type() (Database.query.Connector method)
get_reactions() (Database.query.Connector method)
get_reactions_based_on_type() (Database.query.Connector method)
get_reactions_in_model() (Database.query.Connector method)
get_reference() (Database.query.Connector method)
get_rxn_components() (Database.build_user_rxns_db.AddUserRxns2DB method)
get_SMILES() (Visualization_graphviz.reaction_files.ReactionFiles method)
get_smiles_from_name() (Visualization_graphviz.reaction_files.ReactionFiles method)
get_solvents() (Database.query.Connector method)
get_stoichiometry() (Database.query.Connector method)
get_stoichometry() (Database.build_user_rxns_db.AddUserRxns2DB method)
get_tanimoto_score() (Parser.structure_similarity.TanimotoStructureSimilarity method)
get_target_name() (Visualization_chemdraw.reaction_files.ReactionFiles method)
get_temperature() (Database.query.Connector method)
get_time() (Database.query.Connector method)
get_uniq_metabolic_clusters() (Database.query.Connector method)
get_x() (Visualization_chemdraw.cdxml_elements.ELEMENT method)
get_y() (Visualization_chemdraw.cdxml_elements.ELEMENT method)
get_yield() (Database.query.Connector method)
GraphDot (class in Visualization_graphviz.SP_Graph_dot)
I
identify_internal_rxns() (ShortestPath.integerprogram_pulp.IntergerProgram method)
identify_overlapping_ids() (Database.remove_duplicate_cpds.OverlappingCpdIDs method)
initial_A_matrix() (ShortestPath.constraints.ConstructInitialLP method)
initial_reaction_constraints() (ShortestPath.constraints.ConstructInitialLP method)
initiate_cycle_check() (ShortestPath.integerprogram_pulp.IntergerProgram method)
initiate_internal_cycle_check() (ShortestPath.integerprogram_pulp.IntergerProgram method)
initiate_multiple_solutions() (ShortestPath.integerprogram_pulp.IntergerProgram method)
insert_comprehensive_model_results_2_db() (in module Database.build_kbase_db)
insert_individual_model_results_2_db() (in module Database.build_kbase_db)
IntergerProgram (class in ShortestPath.integerprogram_pulp)
internal_compound_attr() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
ip_calculate() (ShortestPath.integerprogram_pulp.IntergerProgram method)
is_reversible() (Database.query.Connector method)
is_reversible_all() (Database.query.Connector method)
iter() (Visualization_chemdraw.cdxml_elements.ELEMENT method)
K
k_number_paths() (ShortestPath.integerprogram_pulp.IntergerProgram method)
kegg2pubcheminchi() (in module Database.build_kbase_db)
(in module Database.build_modelseed)
L
list_nodes() (Visualization_chemdraw.reaction_files.Tree method)
load_complete_genomes() (Database.build_modelseed.BuildModelSeed method)
load_file_info_2_db() (in module Database.build_kbase_db)
load_pulp_row_constraints() (ShortestPath.constraints.ConstructInitialLP method)
load_reaction_variables() (ShortestPath.constraints.ConstructInitialLP method)
load_stoichometry_for_met() (in module ShortestPath.constraints)
LoadIntoDB (class in Database.build_modelseed)
M
MetaCyc (class in Database.build_metacyc_db)
modelinfo_opener() (Parser.read_targets.Readfile method)
multiple_copies_of_rxns() (Database.build_metacyc_db.MetaCyc method)
multiple_optimal_solution() (ShortestPath.integerprogram_pulp.IntergerProgram method)
multiple_optimal_solution_internal() (ShortestPath.integerprogram_pulp.IntergerProgram method)
N
Node (class in Visualization_chemdraw.reaction_files)
O
offset_ids() (Visualization_chemdraw.cdxml_elements.COMPOUND method)
open_atlas_files() (in module Database.build_ATLAS_db)
open_file() (in module Database.build_SPRESI_db)
open_mspfile() (Database.build_MINE_db.BuildMINEdb method)
open_translation_file() (in module Database.build_kbase_db)
(in module Database.build_modelseed)
open_user_file() (Database.build_user_rxns_db.AddUserRxns2DB method)
OptimizeTarget (class in FBA.optimize_target)
order_of_paths() (Visualization_chemdraw.reaction_files.ReactionFiles method)
(Visualization_graphviz.reaction_files.ReactionFiles method)
Output (class in Parser.generate_output)
output_compound_natively_present_in_target_organism() (Parser.generate_output.Output method)
output_essential_reactions() (Parser.generate_output.Output method)
output_FBA() (Parser.generate_output.Output method)
output_FBA_KOs() (Parser.generate_output.Output method)
output_final_targets() (Parser.generate_output.Output method)
output_open_paths_all_organism_file() (Parser.generate_output.Output method)
output_paths_all_organisms() (Parser.generate_output.Output method)
output_raw_solutions() (Parser.generate_output.Output method)
output_shortest_paths() (Parser.generate_output.Output method)
output_theoretical_yield() (Parser.generate_output.Output method)
output_timer() (Parser.generate_output.Output method)
OverlappingCpdIDs (class in Database.remove_duplicate_cpds)
P
parse_cdxml() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
parse_data_sbmlfile() (in module Database.build_kbase_db)
parse_file() (in module Database.build_SPRESI_db)
parse_solution() (in module FBA.retrieve_producable_mets)
Parser (module)
Parser.compute_tanimoto (module)
Parser.generate_output (module)
Parser.read_targets (module)
Parser.structure_similarity (module)
perform_knockouts() (FBA.optimize_target.OptimizeTarget method)
process_cobra_model() (Database.build_modelseed.BuildModelSeed method)
process_compartments() (in module Database.build_kbase_db)
process_compound() (in module Database.build_KEGG_db)
process_compounds() (in module Database.build_kbase_db)
process_reaction() (in module Database.build_KEGG_db)
process_reactions() (in module Database.build_ATLAS_db)
(in module Database.build_kbase_db)
process_rxntext() (in module Database.build_SPRESI_db)
process_substrates() (in module Database.build_ATLAS_db)
process_targets() (Parser.structure_similarity.TanimotoStructureSimilarity method)
R
RDF_Reader() (in module Database.build_SPRESI_db)
reaction_constraints_ignore_reactions() (ShortestPath.constraints.ConstructInitialLP method)
reaction_constraints_include_reactions() (ShortestPath.constraints.ConstructInitialLP method)
reaction_constraints_pulp() (ShortestPath.constraints.ConstructInitialLP method)
ReactionFiles (class in Visualization_chemdraw.reaction_files)
(class in Visualization_graphviz.reaction_files)
read_metacyc_file() (Database.build_metacyc_db.MetaCyc method)
Readfile (class in Parser.read_targets)
reformat_inchi() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
remove_compartment_info_from_cpdID() (Parser.structure_similarity.TanimotoStructureSimilarity method)
remove_modifications() (FBA.optimize_target.OptimizeTarget method)
retrieve_compartment_4_compartment() (Database.build_metacyc_db.MetaCyc method)
retrieve_exact_inchi_values() (in module Database.build_kbase_db)
(in module Database.build_modelseed)
retrieve_fingerprints() (Parser.structure_similarity.TanimotoStructureSimilarity method)
retrieve_metabolic_clusters() (in module Database.build_kbase_db)
retrieve_promiscuous_mets() (in module Visualization_chemdraw.exclude_cpds)
retrieve_rxn_info() (Database.build_metacyc_db.MetaCyc method)
retrieve_stoichiometry() (ShortestPath.constraints.ConstructInitialLP method)
RetrieveActiveRxnsCompounds() (in module FBA.retrieve_producable_mets)
run_cycle_check() (ShortestPath.integerprogram_pulp.IntergerProgram method)
run_fba() (FBA.optimize_target.OptimizeTarget method)
run_flux() (FBA.build_model.BuildModel method)
run_glpk() (ShortestPath.integerprogram_pulp.IntergerProgram method)
rxn_translator() (Database.build_metacyc_db.MetaCyc method)
S
sc_graph() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
scale() (Visualization_chemdraw.cdxml_elements.COMPOUND method)
set_color() (Visualization_chemdraw.cdxml_elements.BOX method)
(Visualization_chemdraw.cdxml_elements.ELEMENT method)
(Visualization_chemdraw.cdxml_elements.TEXT method)
(Visualization_chemdraw.cdxml_elements.TRANSITION method)
set_dimensions() (Visualization_chemdraw.cdxml_elements.COMPOUND method)
set_FBA() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
set_id() (Visualization_chemdraw.cdxml_elements.ELEMENT method)
set_label() (Visualization_chemdraw.cdxml_elements.TEXT method)
set_lp_problem() (ShortestPath.integerprogram_pulp.IntergerProgram method)
set_objective_function() (FBA.build_model.BuildModel method)
(FBA.optimize_target.OptimizeTarget method)
(ShortestPath.integerprogram_pulp.IntergerProgram method)
set_objective_function_internal() (ShortestPath.integerprogram_pulp.IntergerProgram method)
set_output_label() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
set_products() (Visualization_chemdraw.cdxml_editor.CDXML_Editor method)
set_root() (Visualization_chemdraw.reaction_files.Tree method)
set_row_bounds() (ShortestPath.integerprogram_pulp.IntergerProgram method)
set_weight() (ShortestPath.integerprogram_pulp.IntergerProgram method)
set_x() (Visualization_chemdraw.cdxml_elements.BOX method)
(Visualization_chemdraw.cdxml_elements.ELEMENT method)
set_y() (Visualization_chemdraw.cdxml_elements.BOX method)
(Visualization_chemdraw.cdxml_elements.ELEMENT method)
ShortestPath (module)
ShortestPath.constraints (module)
ShortestPath.extractinfo (module)
ShortestPath.integerprogram_pulp (module)
strain_check() (Parser.read_targets.Readfile method)
synthetic_compound_attr() (Visualization_graphviz.SP_Graph_dot.GraphDot method)
T
tanimoto() (in module Parser.compute_tanimoto)
TanimotoStructureSimilarity (class in Parser.structure_similarity)
test_db_4_error() (in module Database.query)
TEXT (class in Visualization_chemdraw.cdxml_elements)
track_final_cpd (Parser.structure_similarity.TanimotoStructureSimilarity attribute)
TRANSITION (class in Visualization_chemdraw.cdxml_elements)
Translate (class in Database.build_metacyc_db)
Tree (class in Visualization_chemdraw.reaction_files)
U
update_position() (Visualization_chemdraw.cdxml_elements.ARC method)
(Visualization_chemdraw.cdxml_elements.ARROW method)
(Visualization_chemdraw.cdxml_elements.BOX method)
(Visualization_chemdraw.cdxml_elements.ELEMENT method)
V
verbose_print() (in module Database.build_metacyc_db)
(in module Database.build_modelseed)
(in module FBA.build_model)
(in module FBA.optimize_target)
(in module Parser.generate_output)
(in module Parser.structure_similarity)
(in module ShortestPath.integerprogram_pulp)
Visualization_chemdraw (module)
Visualization_chemdraw.cdxml_editor (module)
Visualization_chemdraw.cdxml_elements (module)
Visualization_chemdraw.exclude_cpds (module)
Visualization_chemdraw.reaction_files (module)
Visualization_graphviz (module)
Visualization_graphviz.chempyutilgraph_edit (module)
Visualization_graphviz.reaction_files (module)
Visualization_graphviz.SP_Graph_dot (module)
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