Molfilefinder

getMissingDrugMolForm(metabolite_structure, molFileDirectory, startSearch, endSearch)[source]

Retrieves mol files from DrugBank using DrugBank IDs

It relies on getMolFileFromDrugbank.m and updates the metabolite structure to record which entries have an associated mol file.

USAGE:

[metabolite_structure] = getMissingDrugMolForm (metabolite_structure, molFileDirectory, startSearch, endSearch)

INPUTS:

  • metabolite_structure – Metabolite structure

  • molFileDirectory – Directory where the mol files should be stored

OPTIONAL INPUTS:

  • startSearch – Numeric index where the search starts in the metabolite structure (default: 1)

  • endSearch – Numeric index where the search ends in the metabolite structure (default: all metabolites)

OUTPUTS:

metabolite_structure – Updated metabolite structure

getMissingHMDBMolForm(metabolite_structure, molFileDirectory, retrievePotHMDB, startSearch, endSearch)[source]

Obtains mol files for metabolite structure entries that have HMDB IDs

Uses getMolFileFromHMDB.m to obtain mol files for entries with HMDB IDs, and can optionally search HMDB by metabolite name to find new HMDB entries (only perfect matches are considered). See retrievePotHitsHMDB.m for more details.

USAGE:

[metabolite_structure] = getMissingHMDBMolForm (metabolite_structure, molFileDirectory, retrievePotHMDB, startSearch, endSearch)

INPUTS:

  • metabolite_structure – Metabolite structure

  • molFileDirectory – Directory where the mol files should be stored

OPTIONAL INPUTS:

  • retrievePotHMDB – If 1 (default), also query HMDB by metabolite name to find new HMDB entries (this can be time consuming)

  • startSearch – Numeric index where the search starts in the metabolite structure (default: 1)

  • endSearch – Numeric index where the search ends in the metabolite structure (default: all metabolites)

OUTPUTS:

metabolite_structure – Updated metabolite structure

getMolFileFromDrugbank(metAbbr, drugbank, directory)[source]

Connects to DrugBank and retrieves the mol file for a metabolite

The retrieved mol file is saved in the specified directory under the given metAbbr name. Two DrugBank endpoints are tried, for metabolites and for small molecule drugs respectively: https://go.drugbank.com/structures/metabolites/DBMET01243.mol https://go.drugbank.com/structures/small_molecule_drugs/DB05478.mol

USAGE:

[outFile] = getMolFileFromDrugbank (metAbbr, drugbank, directory)

INPUTS:

  • metAbbr – Metabolite abbreviation

  • drugbank – DrugBank ID

  • directory – Full path where the mol files should be saved (without final /)

OUTPUTS:

outFile – Full path to the saved mol file, or ‘’ if retrieval failed

getMolFilesMultipleSources(metabolite_structure, molFileDirectory, startSearch, endSearch, source)[source]

Obtains mol files from different resources for a metabolite structure

For details please check obtainMetStructures.m.

USAGE:

[metabolite_structure, molCollectionReport] = getMolFilesMultipleSources (metabolite_structure, molFileDirectory, startSearch, endSearch, source)

INPUTS:

  • metabolite_structure – Metabolite structure

  • molFileDirectory – Folder where the mol files should be deposited

OPTIONAL INPUTS:

  • startSearch – Numeric index where the search starts in the metabolite structure (default: 1)

  • endSearch – Numeric index where the search ends in the metabolite structure (default: all metabolites)

  • source – Resource to obtain the mol file from (default: all resources): ‘inchi’ or ‘smiles’ (require Open Babel), ‘kegg’, ‘hmdb’, ‘pubchem’, or ‘chebi’

OUTPUTS:

  • metabolite_structure – Updated metabolite structure

  • molCollectionReport – Report of the mol file collection process