code: public ISimpleChemObjectReader createReader(Reader input) throws IOException {
          if (!(input instanceof BufferedReader)) {
              input = new BufferedReader(input);
          }
          IChemFormat chemFormat = formatFactory.guessFormat((BufferedReader) input);
          ISimpleChemObjectReader coReader = createReader(chemFormat);
          try {
              coReader.setReader(input);
          } catch (Exception exception) {
              logger.error("Could not set the Reader source: ", exception.getMessage());
              logger.debug(exception);
          }
          return coReader;
      }
docs: Detects the format of the Reader input, and if known, it will return
  a CDK Reader to read the format. This method is not able to detect the
  format of gziped files. Use createReader(InputStream) instead for such
  files.
  
  @see #createReader(InputStream)