Generatemetinfo

convertInchiString2format(inchiString, format)

Converts an InChI string into a given format (either inchiKey or smiles) It relies on obabel (Open Babel) being installed. Installation on mac with Homebrew: brew install open-babel.

USAGE:

[result] = convertInchiString2format (inchiString, format)

INPUTS:

• inchiString – InChI string to be converted

• format – Target format, either ‘inchiKey’ or ‘smiles’

OUTPUTS:

result – Converted InChI string in the format defined by format

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

Adds InChI strings to metabolite structure entries when mol files are available

For each entry that has a mol file (in folder) but no InChI string yet, the InChI string is generated. Optionally, the InChI key, the SMILES string, and the metabolite formula and charge are also generated. Relies on obabel.

USAGE:

[metabolite_structure, IDsAdded, InchiKeyList, InchiStringList] = generateInchiFromMol (metabolite_structure, folder, inchiKey, smiles, formula, startSearch, endSearch)

INPUTS:

• metabolite_structure – Metabolite structure

• folder – Folder containing the mol files

OPTIONAL INPUTS:

• inchiKey – If 1 (default), the InChI key is generated from the mol file

• smiles – If 1 (default), the SMILES string is generated from the mol file

• formula – If 1 (default), the formula and charge are generated

• 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

• IDsAdded – List of IDs added to the metabolite structure

• InchiKeyList – List of InChI keys added

• InchiStringList – List of InChI strings added

generateInchiKeysSmilesFromInchiStrings(metabolite_structure)

Generates missing InChI keys and SMILES strings from available InChI strings

Searches the metabolite structure for entries where the InChI key or SMILES string is missing but the InChI string is available, and generates the InChI key/SMILES using Open Babel (obabel).

USAGE:

[metabolite_structure, IDsAdded] = generateInchiKeysSmilesFromInchiStrings (metabolite_structure)

INPUTS:

metabolite_structure – Metabolite structure

OUTPUTS:

• metabolite_structure – Updated metabolite structure

• IDsAdded – List of added InChI keys/SMILES strings

getInchiString2ChargedFormula(metList, inchiStringList)

Computes the charged formula and metabolite charge at pH 7 from InChI strings

It requires ChemAxon and Open Babel. The provided InChI string is assumed to describe the neutral metabolite; if it does not, metFormulaNeutral instead reflects the formula provided with the InChI string.

USAGE:

[metFormulaNeutral, metFormulaCharged, metCharge] = getInchiString2ChargedFormula (metList, inchiStringList)

INPUTS:

• metList – List of metabolite abbreviations

• inchiStringList – List of InChI strings (same order as metList)

OUTPUTS:

• metFormulaNeutral – Neutral metabolite formula (as provided in the InChI string)

• metFormulaCharged – Charged metabolite formula (at pH 7)

• metCharge – Metabolite charge (double, at pH 7)