Generatemetinfo

convertInchiString2format(inchiString, format)

function [result] = convertInchiString2format(inchiString,format) This function converts an inchiString into a given format (either inchikey or smiles). It relies on obabel being installed. obabel installation on mac with home brew: brew install open-babel

INPUT inchiString inchiString format either ‘inchiKey’ or ‘smiles’

OUTPUT result converted inchiString in format as defined by ‘format’

Ines Thiele 2020/2021

generateInchiFromMol(metabolite_structure, folder, inchiKey, smiles, formula, startSearch, endSearch)

This function adds inchistrings to the metabolite structure entries if mol files are available (in folder) and no inchistring is present in metabolite structure for a given entry. It also calculated inchikeys and smiles if desired.

INPUT metabolite_structure metabolite structure folder folder containing the mol files inchiKey if 1 (default), then inchiKey will be generated

from mol file

smiles if 1 (default), then smiles will be generated

from mol file

formula if 1 (default), then inchiKey will be generated

from inchistring file

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 IDsAddeed List of IDs added to the metabolite structure InchiKeyList List of inchikeys added InchiStringList List of inchistrings added

Ines Thiele, 2020-2021

generateInchiKeysSmilesFromInchiStrings(metabolite_structure)

This function searches the metabolite structure for instances where the inchiKey/smiles are missing but the inchiString is available and generates the inchiKey/smiles using openBable.

INPUT metabolite_structure metabolite structure

OUTPUT metabolite_structure updated metabolite structure IDsAdded added inchiKeys/smiles

Ines Thiele 01/2021

getInchiString2ChargedFormula(metList, inchiStringList)

This function computes the charged formula and metabolite charge at ph7 from a list of inchiStrings. It requires ChemAxxon and openBabel

INPUT metList List of metabolite abbr inchiStringList List of inchiStrings (same order as metList), the

function assumes that the provided inchiString is given for the neutral metabolite. If this is not the case, it still works, however, metFormulaNeutral represents not the neutral formula but the one provided with the inchiString.

OUTPUT metFormulaNeutral List of neutral metabolite formula (as provided in

the inchiString)

metFormula List of charged metabolite formula (at ph7) metCharge List of metabolite charges (double, at ph7)

Ines Thiele, 09/2021