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kegg2mol(cid, molfileDir, mets, takeMajorMS, pH, takeMajorTaut)

Retreive molfiles from the KEGG Compound database.

kegg2mol(cid,molfileDir,mets,takeMajorMS,pH,takeMajorTaut)

INPUTS cid m x 1 array of KEGG Compound identifiers.

OPTIONAL INPUTS molfileDir Path to directory where molfiles will be saved. Default

is molfilesFromKegg.

mets m x 1 array of metabolite identifiers. Used to name

molfiles. KEGG Compound ID will be used if mets is omitted.

takeMajorMS {(0),1}. If 0 (default), molfiles will be downloaded

directly from KEGG. If 1, they will save as the major microspecies at the pH specified in input variable pH. Computing major microspecies requires ChemAxon’s calculator plugins (cxcalc).

pH pH for computing major microspecies. takeMajorTaut {0,(1)}. If 1 (default), molfiles will be saved as the

major tautomers of the major microspecies at the specified pH.

WRITTEN OUTPUTS One molfile for each metabolite with a KEGG Compound ID.

modelMetabolitesToSDF(model, InChI)

write out an SDF which is effectively a set of mol files concatenated in a flat file with extra data headers

SDF format spec http://www.symyx.com/downloads/public/ctfile/ctfile.jsp

INPUT model model structure

OPTIONAL INPUT InChI m x 2 cell array of InChI strings for each metabolite

InChI{i,1} is a metabolite abbreviation (no compartment) InChi{i,2} is a metabolite InChI string

OPTIONAL OUTPUT model.mets(m).InChI InChI mapped to model if provided as imput model.met(m).formulaInChI Chemical formula as given in InChI Ronan M.T. Fleming

mol2sdf(mets, molfileDir, sdfFileName, includeRs)

Concatenates molfiles in molfileDir into one SDF file.

metList = mol2sdf(mets,molfileDir,sdfFileName)

INPUTS mets mx1 cell array of metabolite identifiers (e.g., BiGG

abbreviations)

molfileDir Path to directory containing molfiles for metabolites

in mets. Molfile names should match the metabolite identifiers in mets without compartment assignments.

OPTIONAL INPUTS sdfFileName Name of SDF file. Default is MetStructures.sdf. includeRs {0,(1)}. If 0, variable structures such as R groups and

repeat units will not be included in SDF.

OUTPUTS metList Cell array listing metabolites in SDF. noMolMetList Cell array listing metabolites without mol file.

WRITTEN OUTPUTS sdfFileName.sdf SDF with metabolite structures in same order as in

metList. Metabolite identifiers in the SDF are the same as in MetList.

Ronan M.T. Fleming Hulda SH, Nov. 2012 Changed output format from CDF to SDF. Renamed

function. Simplified code.