code: private IChemFile readChemFile(IChemFile file) throws IOException {
          IChemSequence seq = file.getBuilder().newInstance(IChemSequence.class);
          IChemModel model = file.getBuilder().newInstance(IChemModel.class);
          ICrystal crystal = readCrystal(file.getBuilder().newInstance(ICrystal.class));
          model.setCrystal(crystal);
          seq.addChemModel(model);
          file.addChemSequence(seq);
          return file;
      }
docs: Read the ShelX from input. Each ShelX document is expected to contain
  one crystal structure.
  
  @return a ChemFile with the coordinates, charges, vectors, etc.