code: @Override
      public List<IAtomType> readAtomTypes(IChemObjectBuilder builder) throws IOException {
          List<IAtomType> atomTypes;
          if (ins == null) throw new IOException("There was a problem getting an input stream");
          OWLAtomTypeReader reader = new OWLAtomTypeReader(new InputStreamReader(ins));
          atomTypes = reader.readAtomTypes(builder);
          for (IAtomType atomType : atomTypes) {
              if (atomType == null) {
                  logger.debug("Expecting an object but found null!");
              }
          }
          return atomTypes;
      }
docs: Reads the atom types from the OWL based atom type list.
  
  @param builder IChemObjectBuilder used to construct the IAtomType's.
  @throws        IOException when a problem occurred with reading from the InputStream
  @return        A List with read IAtomType's.