molFiles

kegg2mol(cid, molfileDir, mets, takeMajorMS, pH, takeMajorTaut)[source]

Retrieve molfiles from the KEGG Compound database.

Usage

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

Input

  • 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 output - One molfile for each metabolite with a KEGG Compound ID.

If takeMajorMS = 1 - approximately 2 seconds per kegg id. If takeMajorMS = 0 - approximately 0.3 seconds per kegg id.