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createInChIStruct(mets, sdfFileName)

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

inchi = 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.

OUTPUTS inchi 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.

Hulda SH, Nov. 2012

getFormulaAndChargeFromInChI(inchi)

[formula,charge] = getFormulaAndChargeFromInChI(inchi)

INPUT inchi…….Nonstandard IUPAC InChI for a particular pseudoisomer of a

metabolite

OUTPUTS formula….The chemical formula for the input pseudoisomer charge…..The charge on the input pseudoisomer

sdf2inchi(sdfFileName, options)

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

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

INPUTS 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’).

Hulda SH, Nov. 2012