code: public static List<SecStrucState> parseInputStream(InputStream dsspIs,
  			Structure structure, boolean assign)
  					throws IOException, StructureException {
  
  		BufferedReader reader = new BufferedReader(new InputStreamReader(dsspIs));
  		return generalParse(reader, structure, assign);
  	}
docs: Parse a DSSP output file and return the secondary structure
  annotation as a List of {@link SecStrucState} objects.
  
  @param dsspIs an InputStream to a DSSP file
  @param structure Structure object associated to the dssp
  @param assign assigns the SS to the structure if true
  @return a List of SS annotation objects
  @throws StructureException
  @throws IOException