Metabolites

addMetInfoInCBmodel(model, inputData, replace)

Integrates metabolite data from an external file and incorporates it into the COBRA model.

USAGE

[newModel, hasEffect] = addMetInfoInCBmodel (model, inputData, replace)

INPUTS

• model – COBRA model with following fields:

  • .S - The m x n stoichiometric matrix for the

    metabolic network.

  • .mets - An m x 1 array of metabolite identifiers.

• inputData

OPTIONAL INPUTS

replace – If the new ID should replace an existing ID, this logical value indicates so (default: false).

OUTPUTS

• newModel – COBRA model with updated identifiersCOBRA model with the identifiers updated.

• hasEffect

metDatabaseStatus(model, metDir)

Prints the status of metabolite structure in a database in relation to a COBRA model.

USAGE

[summary, status] = metDatabaseStatus (model, metDir)

INPUTS

• model – COBRA model with following fields: * .mets - An m x 1 array of metabolite identifiers. * .metFromulas - An m x 1 array of metabolite flormulas. * .metCharges - An m x 1 vector of metabolite charges. * .identifiers - An m x 1 array of metabolite identifiers. * .inchi - An m x 1 array of metabolite identifiers. * .kegg - An m x 1 array of metabolite identifiers. * .chebi - An m x 1 array of metabolite identifiers. * .hmdb - An m x 1 array of metabolite identifiers. * .pubchem - An m x 1 array of metabolite identifiers.

• metDir – Directory of the metabolite database (MDL MOL files)

OUTPUTS

• summary – Summary of the metabolite database and the identifiers.

• status – Table with the status of each metabolite in the database.

metaboliteStructuresTable(metDir, saveDir)

This fucntion creates a table of different representations of a metabolite structure including smiles, inchi and inchikey,

USAGE

metTable = metaboliteStructuresTable (metDir, saveDir)

INPUT

metDir – String with the directory containing mol files

OPTIONAL INPUTS

saveDir – String with the directory where the table format will be saved. If is empty, the format is not saved.

obtainMetStructures(model, metList, outputDir, sources)

Obtain MDL MOL files from various databases, including KEGG, HMDB, ChEBI, and PubChem. Alternatively, openBabel can be used to convert InChI strings or SMILES in MDL MOL files.

USAGE:

molCollectionReport = obtainMetStructures(model, mets, sources, standardisationApproach)

INPUTS

model – COBRA model with following fields:

• .S - The m x n stoichiometric matrix for the metabolic network.

• .mets - An m x 1 array of metabolite identifiers.

• .metInChIString - An m x 1 array of metabolite identifiers.

• .metSmiles - An m x 1 array of metabolite identifiers.

• .metVMHID - An m x 1 array of metabolite identifiers.

• .metCHEBIID - An m x 1 array of metabolite identifiers.

• .metKEGGID - An m x 1 array of metabolite identifiers.

• .metPubChemID - An m x 1 array of metabolite identifiers.

• .metHMDBID - An m x 1 array of metabolite identifiers.

• .metDrugbankID - An m x 1 array of metabolite identifiers.

• .metLipidmassID - An m x 1 array of metabolite identifiers.

OPTIONAL INPUTS

• mets – List of metabolites to be download (Default: All)

• outputDir – Directory that will contain the obtained metabolite structures.

• sources –

  Sources where the MOL files will be obtained (Default: all).

  The sources supported are:

  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/) 7.- ‘drugbank’ (https://go.drugbank.com/) 8.- ‘lipidmass’ (https://www.lipidmaps.org/)

OUTPUTS

• molCollectionReport – Report of the obtained MDL MOL files

  • .metList - List of metabolites to be download

  • .sources -list of sources of metabolite structures

  • .structuresObtained -Total of metabolite structures obtained.

  • .structuresObtainedPerSource -Boolean table with the metabolite

    structures obtained by source.

  • .databaseCoverage -Table indicating the coverage of metabolites

    obtained by each of the sources.

  • .idsToCheck -Id source from which no molecular structures could

    be obtained due to a webTimeout, conversion error, or inconsistent id.

• newMolFilesDir – directory where new mol files were written, subdirectories for each source.

standardiseMolDatabase(molDir, metList, standardisedDir, standardisationApproach)

Standardize an MDL MOL file directory by representing the reaction using normal chemical graphs, hydrogen suppressed chemical graphs, and chemical graphs with protonated molecules. The function also updates the header with the standardization information. It makes use of ChemAxon’s standardizer and openBabel.

USAGE:

[standardised, nonStandardised, InChIs, SMILES] = standardiseMolDatabase(molDir, standardisedDir, standardiseMolFiles)

INPUTS

molDir – Path to directory that contain the MDL MOL files to be standardised.

OPTIONAL INPUTS

• metList – 1 x n lest of metabolites to standardise

• standardisedDir – Path to directory that will contain the standardised MDL MOL files (default: current directory).

• standardisationApproach – String contianing the type of standarization for the moldecules (default: ‘explicitH’ if openBabel is installed, otherwise ‘basic’)

  ‘explicitH’ - Normal chemical graphs. ‘implicitH’ - Hydrogen suppressed chemical graphs. ‘neutral’ - Neutral molecules ‘basic’ - Updating the header.

OUTPUTS

• standardisationReport – Struct array with the standarization report:

  • .standardised: list of standardised metabolite structures

  • .nonStandardised: list of metabolite structures that were not

    standardised.

  • .InChIs: list of InChIs from the obtained metabolite

    structures

  • .SMILES: list of SMILES from the obtained metabolite

    structures

  • .InChIKeys: list of InChIKeys from the obtained metabolite

    structures

• A standardised molecular structures database