Groovy Bioclipse script

// To run in Bioclipse groovy console write:
// evaluate(ui.readFile("/Bioclipse_project_MM/makeSmilesFile.groovy"))

dataIn = new java.net.URL("platform:/resource/Bioclipse_project_MM/solubilityData.csv")
smilesIn = new java.net.URL("platform:/resource/Bioclipse_project_MM/solubilitySMILES.txt")

def map = new java.util.HashMap();

( dataIn.openStream() ).eachLine { line ->
    sid = line.split(",")[0];
    sol = line.split(",")[7];
    if (map.containsKey(sid)) {
        print("Found " + sid + " twice");
    }
    map.put(sid, sol)
}

file = new File( ui.newFile("Bioclipse_project_MM/solubility.smi").getRawLocation().toString() )
i = 0
( smilesIn.openStream() ).eachLine { line ->
    sid = line.split("\t")[0];
    SMILES = line.split("\t")[1];

    file << (SMILES + ", " + ( Double.parseDouble(map.get(sid)) / cdk.calculateMass(cdk.fromSMILES(SMILES) ) / 1000) + "\n");
    if ( ++i%100 == 0 ) {
        print(i + " Done. \n");
    }
}
print("All Done.")