mdlCheck.groovy

// CDK 1.3.5

import java.io.*;
import org.openscience.cdk.io.*;
import org.openscience.cdk.Molecule;

class ErrorHandler implements IChemObjectReaderErrorHandler {
  public void handleError(String message) {
    println message;
  };
  public void handleError(String message, Exception exception) {
    println message + "\n  -> " + exception.getMessage();
  };
  public void handleError(String message, int row, int colStart, int colEnd) {
    print "location: " + row + ", " + colStart + "-" + colEnd + ": ";
    println message;
  };
  public void handleError(String message, int row, int colStart, int colEnd, Exception exception) {
    print "location: " + row + ", " + colStart + "-" + colEnd + ": ";
    println message + "\n  -> " + exception.getMessage();
  };
}

reader = new MDLV2000Reader(new FileReader(args[0]))
reader.setErrorHandler(new ErrorHandler());
mol = reader.read(new Molecule());