code: protected void newAtomData() {
          atomCounter = 0;
          elsym = new ArrayList<String>();
          elid = new ArrayList<String>();
          eltitles = new ArrayList<String>();
          formalCharges = new ArrayList<String>();
          partialCharges = new ArrayList<String>();
          isotope = new ArrayList<String>();
          atomicNumbers = new ArrayList<String>();
          exactMasses = new ArrayList<String>();
          x3 = new ArrayList<String>();
          y3 = new ArrayList<String>();
          z3 = new ArrayList<String>();
          x2 = new ArrayList<String>();
          y2 = new ArrayList<String>();
          xfract = new ArrayList<String>();
          yfract = new ArrayList<String>();
          zfract = new ArrayList<String>();
          hCounts = new ArrayList<String>();
          atomParities = new ArrayList<String>();
          parityARef1 = new ArrayList<String>();
          parityARef2 = new ArrayList<String>();
          parityARef3 = new ArrayList<String>();
          parityARef4 = new ArrayList<String>();
          atomAromaticities = new ArrayList<String>();
          atomDictRefs = new ArrayList<String>();
          spinMultiplicities = new ArrayList<String>();
          occupancies = new ArrayList<String>();
          atomCustomProperty = new HashMap<Integer, List<String>>();
      }
docs: Clean all data about read atoms.