Bioclipse code to check chemical compounds with isomeric SMILES and no InChI

curation1.groovy

// Copyright (C) 2017 Egon Willighagen
// MIT license

// see https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Tools#Chemical_compound_without_InChI

/* results (2017-10-29):

  Number of missing InChIs: 2098
  InChI too long: 1736
  With undefined stereo: 348
  Bad SMILES: 2
  Compound classes: 12
*/

query = """
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wd: <http://www.wikidata.org/entity/>
SELECT ?compound ?smiles WHERE {
  ?compound wdt:P31 wd:Q11173 ;
            wdt:P2017 ?smiles .
  MINUS {?compound wdt:P234 ?d }
}
"""

service = "https://query.wikidata.org/bigdata/namespace/wdq/sparql"
results = rdf.sparqlRemote(service, query)

qsFile = "/Wikidata/curation1.quickstatements"
def renewFile(file) {
  if (ui.fileExists(file)) ui.remove(file)
  ui.newFile(file)
  return file
}
renewFile(qsFile)

tooLong = 0
undefinedStereo = 0
badSmiles = 0
compoundClass = 0
for (i=1;i<=results.rowCount;i++) {
// for (i=1;i<=2;i++) {
  rowVals = results.getRow(i)
  item = rowVals[0].substring(3)
  smiles = rowVals[1]
  if (!smiles.contains("*")) { // skip compound classes
    try {
      mol = cdk.fromSMILES(smiles)
      inchiObj = inchi.generate(mol)
      inchiShort = inchiObj.value.substring(6)
      key = inchiObj.key
      if (!inchiShort.contains("?")) { // skip undefined stereochemistry
        if (inchiShort.length() <= 400) {
          statement = """
            CREATE
            $item\tP31\tQ11173$paperProv
            $item\tDen\t\"chemical compound\"$paperProv
            $item\t$smilesProp\t\"$smiles\"
            $item\tP274\t\"$formula\"
            $item\tP234\t\"$inchiShort\"
            $item\tP235\t\"$key\"
            $pubchemLine
          """
          ui.append(qsFile, statement + "\n")
        } else {
          // println "$item has an InChI that is too long: $inchiShort"
          tooLong++
        }
      } else {
        // println "$item has undefined stereochemistry(?): $inchiShort"
        undefinedStereo++
      }
    } catch (Exception e) {
      // println "$item has bad SMILES: " + e.message
      badSmiles++
    } // skip bad SMILES
  } else {
    // println "$item is a compound class (has a '*'): $smiles"
    compoundClass++
  }
}

println "Number of missing InChIs: " + results.rowCount
println "InChI too long: $tooLong"
println "With undefined stereo: $undefinedStereo"
println "Bad SMILES: $badSmiles"
println "Compound classes: $compoundClass"

ui.open(qsFile)