Molfilefinder¶
- getMissingDrugMolForm(metabolite_structure, molFileDirectory, startSearch, endSearch)[source]¶
This function trys to retrieve mol files from drug bank using drugbank id’s. It relies on getMolFileFromDrugbank.m.
INPUT metabolite_structure metabolite structure molFileDirectory directory where mol files should be stored startSearch specify where the search should start in the
metabolite structure. Must be numeric (optional, default: all metabolites in the structure will be search for)
- endSearch specify where the search should end in the
metabolite structure. Must be numeric (optional, default: all metabolites in the structure will be search for)
OUTPUT metabolite_structure updated metabolite structure
Ines Thiele 09/21
- getMissingHMDBMolForm(metabolite_structure, molFileDirectory, retrievePotHMDB, startSearch, endSearch)[source]¶
This function uses getMolFileFromHMDB.m to obtain mol files for those metabolite structure entries that have hmdb id’s specified. It also has the option find novel hmdb entries by querying hmdb for the metabolite names. Only perfect matches are considered. See retrievePotHitsHMDB.m for more details.
INPUT metabolite_structure metabolite structure molFileDirectory directory where mol files should be stored retrievePotHMDB default: true (attention: this could be time
consuming)
- startSearch specify where the search should start in the
metabolite structure. Must be numeric (optional, default: all metabolites in the structure will be search for)
- endSearch specify where the search should end in the
metabolite structure. Must be numeric (optional, default: all metabolites in the structure will be search for)
OUTPUT metabolite_structure updated metabolite structure
Ines Thiele 09/21
- getMolFileFromDrugbank(metAbbr, drugbank, directory)[source]¶
This function connects to drugbank and retrieves the mol file, which will be saved in the specified directory under the given metAbbr name
INPUT metAbbr Metabolite abbreviation drugbank Drugbank ID directory Full path where the mol files should be saved (without
final /)
Ines Thiele, 09/2021
- getMolFilesMultipleSources(metabolite_structure, molFileDirectory, startSearch, endSearch, source)[source]¶
This function obtains mol files from differnt resources. For details please check ‘obtainMetStructures.m’.
INPUT metabolite_structure metabolite structure molFileDirectory Folder where mol files should be deposited startSearch specify where the search should start in the
metabolite structure. Must be numeric (optional, default: all metabolites in the structure will be search for)
- endSearch specify where the search should end in the
metabolite structure. Must be numeric (optional, default: all metabolites in the structure will be search for)
- source specify where you want to obtain the mol file from
(default: all resources), options: 1.- ‘inchi’ (requires openBabel) 2.- ‘smiles’ (requires openBabel) 3.- ‘kegg’ (https://www.genome.jp/) 4.- ‘hmdb’ (https://hmdb.ca/) 5.- ‘pubchem’ (https://pubchem.ncbi.nlm.nih.gov/) 6.- ‘chebi’ (https://www.ebi.ac.uk/)
OUTPUT metabolite_structure updated metabolite_structure
Ines Thiele, 09/2021