File[] pklFiles = new File(pklDir).listFiles();
int count = 0;
for (File thePklFile: pklFiles){
count++;
System.out.println("Screening file: " + thePklFile.getName());
PeakMatcher thePeakMatcher = new PeakMatcher((MoleculeSet) inputMolSet, thePklFile, theAdductFile, theTolerance);
theResultMoleculeSet = thePeakMatcher.matchBetweenMoleculeSetAndPeakList();
File theOutFile = new File(theFGDBDir + "\\result_All\\" + thePklFile.getName() + ".sdf" );
SDFWriter.writeSDFile(theResultMoleculeSet, theOutFile);
}
//PeakMatcher thePeakMatcher = new PeakMatcher((MoleculeSet) inputMolSet, thePeakListFile, theAdductFile, theTolerance);