Parser module

Submodules

Parser.compute_tanimoto

Parser.compute_tanimoto.tanimoto(query, target)

Parser.generate_output

class Parser.generate_output.Output(db, output_path, verbose, FBA=False, KO=False, timer_output=False, raw_solutions=True)

Bases: object

Opens and fills output files produced by software

convert_output_2_xlsx()

converts txt files to output files

output_FBA(target_info, org_fbasolution, optimized_fba, comparisonresults, temp)

Outputs reactions and corresponding fluxes for fluxes that change significantly between wild-type FBA simulation (simulation without added reactions) and FBA simulation with added reactions to produce target compound

output_FBA_KOs(target_info, fbasolution, compound_dict, comparisonKOresults, temp)

When reaction knockouts are performed list all reaction that have a significant flux difference from the orignal FBA simulation

output_compound_natively_present_in_target_organism(target_info)

Outputs information if a target compound is already present in an organism

output_essential_reactions(target_compound_ID, target_organism_ID, er)

When reaction knockouts are performed, outputs all reactions that when removed cause decrease in target production

output_final_targets(targets, tan_threshold)

output_open_paths_all_organism_file(target_compound_ID)

Open file to generate file that summarizes how many reactions would need to be added to every organism in the daabase to produce a target organism

output_paths_all_organisms(target_compound_ID, pathlength, orgs, org_names)

Outputs information on the number of reactions that need to be added to an organism to get a target compound, this file is only generated all organisms are being examined to see if they can produce target compound

output_raw_solutions(compound, org_ID, ordered_paths, reactions, externalrxnscount, incpds)

output_shortest_paths(target_info, temp_rxns)

Outputs reactions and compounds that need to be added to an organism to get target compound

output_theoretical_yield(target_compound_ID, target_organism_ID, fbasolution, compounds_dict)

Generates output file with theoretical yields

output_timer(print_statement)

Parser.generate_output.verbose_print(verbose, line)

Parser.read_targets

class Parser.read_targets.Readfile(file_name, db, inchidb=False, compartment='cytosol')

Bases: object

Reads the input file containing target compounds

file_opener()

Opens target file and extracts information

get_db_info()

Retrieve database information for the values in the inputfile

modelinfo_opener()

Get all model information out of the database

strain_check(new_org_format)

Extract all strains for a specified organism

Parser.structure_similarity

class Parser.structure_similarity.TanimotoStructureSimilarity(targets, all_compounds, cytosol, extracellular, verbose, threshold_score=1)

Bases: object

Identifies if compounds are in the database but under a different ID based on structure similarity

calculate_tanimoto_score()

Calculate similarity for compounds that are not in the database

extract_db_cpd_ID(cpdID)

Extract correct database ID for a compound

fill_final_targets(new_target)

get_original_target(tmol)

Obtain original target

get_tanimoto_score(tmol, threshold)

process_targets(targets)

Reformat targets to remove compartment information

remove_compartment_info_from_cpdID(cpd)

retrieve_fingerprints()

Retrieve fingerprints for database compounds and targets

track_final_cpd = None

Remove duplicated targets

Parser.structure_similarity.verbose_print(verbose, line)