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createInChIStruct(mets, sdfFileName)

Convert metabolite structures in an SDF to InChI strings with OpenBabel and map the InChIs to the metabolites

USAGE:

inchiStruct = createInChIStruct (mets, sdfFileName)

INPUTS:

• mets – m x 1 cell array of metabolite identifiers (e.g. BiGG abbreviations)

• sdfFileName – SDF file with structures of the metabolites in mets; the metabolite identifiers in the SDF are assumed to match mets

OUTPUT:

inchiStruct – structure with fields:

• .standard - standard InChIs with no isotope, stereo or charge layers

• .standardWithStereo - standard InChIs with stereo layers

• .standardWithStereoAndCharge - standard InChIs with stereo and charge layers

• .nonstandard - nonstandard InChIs with all layers

getFormulaAndChargeFromInChI(inchi)

Get the chemical formula, number of protons and charge of a pseudoisomer from its InChI

USAGE:

[formula, nH, charge] = getFormulaAndChargeFromInChI (inchi)

INPUT:

inchi – nonstandard IUPAC InChI for a particular pseudoisomer of a metabolite

OUTPUTS:

• formula – chemical formula of the input pseudoisomer

• nH – total number of hydrogens in the protonation form

• charge – charge on the input pseudoisomer

sdf2inchi(sdfFileName, options)

Convert metabolite structures in an SDF to a cell array of InChI strings with OpenBabel

USAGE:

[inchi, metList] = sdf2inchi (sdfFileName, options)

INPUT:

sdfFileName – path to the SDF file

OPTIONAL INPUT:

options – write options for the InChI strings (see the InChI documentation); if omitted, standard InChI is written

OUTPUTS:

• inchi – cell array of InChI strings for the metabolites in the SDF

• metList – cell array of metabolite identifiers (first line of each molfile in the SDF); empty unless the write option t is used (-xt)