New

createInChIStruct(mets, sdfFileName, molFileDir)

Converts metabolite structures in SDF to InChI strings with OpenBabel, and maps InChIs to mets.

USAGE

inchiStruct = createInChIStruct (mets, sdfFileName)

INPUTS

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

• sdfFileName – SDF with structures of metabolites in mets. Metabolite identifiers in the SDF are assumed to be the same as in mets.

OUTPUT

inchiStruct – Structure with following 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 InChI with all layers.

getFormulaAndChargeFromInChI(inchi)

USAGE

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

INPUT

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

OUTPUTS

• formula – The chemical formula for the input pseudoisomer

• nH – The number of total Hydrogen in the actual protonation form

• charge – The charge on the input pseudoisomer (excluding the protonation state)

sdf2inchi(sdfFileName, options)

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

USAGE

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

INPUT

sdfFileName – Path to SDF file.

OPTIONAL INPUTS

options – Write options for InChI strings. See InChI documentation for details. If no options are specified the function will output standard InChI.

OUTPUTS

• inchi – Cell array of InChI strings for metabolites in the SDF file.

• metList – Cell array of metabolite identifiers (first line of each molfile in SDF). Will be empty unless write option t is used (i.e., options >= ‘-xt’).