7. API Reference

• 7.1. Compound I/O
  • export_inchi_rxns()
  • export_kbase()
  • export_mol()
  • export_sdf()
  • export_smiles()
  • export_tsv()
  • import_mol_dir()
  • import_sdf()
  • import_smiles()
• 7.2. Databases
  • MINE
    • MINE.add_reaction_mass_change()
    • MINE.build_indexes()
    • MINE.generate_image_files()
  • establish_db_client()
  • write_compounds_to_mine()
  • write_core_compounds()
  • write_reactions_to_mine()
  • write_targets_to_mine()
• 7.3. Filters
• 7.4. Metabolomics
  • MetabolomicsDataset
    • MetabolomicsDataset.annotate_peaks()
    • MetabolomicsDataset.check_product_of_native()
    • MetabolomicsDataset.enumerate_possible_masses()
    • MetabolomicsDataset.find_db_hits()
    • MetabolomicsDataset.get_rt()
  • Peak
    • Peak.score_isomers()
  • Struct
  • dot_product()
  • get_KEGG_comps()
  • jaccard()
  • ms2_search()
  • ms_adduct_search()
  • read_adduct_names()
  • read_mgf()
  • read_msp()
  • read_mzxml()
  • score_compounds()
  • spectra_download()
• 7.5. Pickaxe
  • Pickaxe
    • Pickaxe.assign_ids()
    • Pickaxe.find_minimal_set()
    • Pickaxe.load_compound_set()
    • Pickaxe.load_pickled_pickaxe()
    • Pickaxe.load_targets()
    • Pickaxe.pickle_pickaxe()
    • Pickaxe.prune_network()
    • Pickaxe.prune_network_to_targets()
    • Pickaxe.save_to_SBML()
    • Pickaxe.save_to_mine()
    • Pickaxe.transform_all()
    • Pickaxe.write_compound_output_file()
    • Pickaxe.write_reaction_output_file()
• 7.6. Reactions
  • transform_all_compounds_with_full()
• 7.7. Rules
  • BNICE()
  • metacyc_generalized()
  • metacyc_generalized_as_df()
  • metacyc_intermediate()
• 7.8. Thermodynamics
• 7.9. Utilities
  • Chunks
    • Chunks.next()
  • StoichTuple
    • StoichTuple.c_id
    • StoichTuple.stoich
  • convert_sets_to_lists()
  • file_to_dict_list()
  • get_atom_count()
  • get_compound_hash()
  • get_dotted_field()
  • get_fp()
  • get_reaction_hash()
  • get_size()
  • mongo_ids_to_mine_ids()
  • neutralise_charges()
  • postsanitize_smiles()
  • prevent_overwrite()
  • save_dotted_field()