New

createInChIStruct(mets, sdfFileName, molFileDir)[source]

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

USAGE:

[inchiStruct, molBool] = createInChIStruct (mets, sdfFileName, molFileDir)

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. If empty, InChIs are built from individual mol files instead

OPTIONAL INPUT:

molFileDir – directory of individual mol files (named <met>.mol), used when sdfFileName is empty

OUTPUTS:

  • 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

  • molBool – m x 1 logical, true where a structure was found for the metabolite

getFormulaAndChargeFromInChI(inchi)[source]

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 – 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)[source]

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’).