calcuateMZs.groovy

bioclipse.requireVersion("2.7.0")
// download all GPML files for a species, and save those in /WikiPathways/data/

// first, calculate m/z values for everything in Wikidata
referenceFile = "/WikiPathways/mz_smiles.tsv"
mzData = new java.util.HashMap()
new File(bioclipse.fullPath(referenceFile)).eachLine { line ->
  tokens = line.tokenize( '\t' )
  if (tokens[0] != "compound") {
    wkid = tokens[0].substring(31)
    smiles = tokens[2].trim()
    try {
      mol = cdk.fromSMILES(smiles)
      mzData.put(wkid, cdk.calculateMajorIsotopeMass(mol)) 
    } catch (Exception exception) {
      println "Error while calculating mass for ${wkid}: " + exception.message
    }
  }
}
mapper = bridgedb.loadRelationalDatabase(bioclipse.fullPath("/WikiPathways/metabolites_20170826.bridge"))

dataMap = bioclipse.fullPath("/WikiPathways/data/human/")
gpmlFiles = new File(dataMap).listFiles()

outputFile = "/WikiPathways/mz_data.tsv"
renewFile(outputFile)

gpmlFiles.each { file ->
  // println "File: " + file.name
  def data = new XmlParser().parse(file)
  def metabolites = data.DataNode.findAll{
    it.'@Type'
  }
  metabolites.each() { node ->
    if (node.'@Type'.contains("Metabolite")) {
      sourceFull = "" + (node.Xref.'@Database'.get(0))
      id         = "" + (node.Xref.'@ID'.get(0))
      // println "$sourceFull .. $id"
      if (sourceFull != null && sourceFull != "" &&
          id != null && id != "") {
        source     = bridgedb.getSourceFromName(sourceFull)
        syscode    = source.systemCode
        xref       = bridgedb.xref(id, syscode)
        wkids      = bridgedb.map(mapper, xref, "Wd")
        if (wkids.size() > 0) {
          // println "Wd items: " + wkids.size()
          wkid = wkids.iterator().next().id
          if (mzData.containsKey(wkid)) {
            // println "Hit for $wkid"
            // println "  Value: " + mzData[wkid]
            ui.append(outputFile, "" + wkid + "\t" + mzData[wkid] + "\n")
          } else {
            println "Got a Wikidata, but no m/z for " + xref
          }
        } else {
          // println "No Wikidata item for " + xref
        }
      }
    }
  }
}