How to use

setObsoleteBehavior

method

in

org.biojava.nbio.structure.io.PDBFileReader

protected Structure loadStructureFromPdbByPdbId(String pdbId) throws IOException, StructureException {
  logger.debug("Loading structure {} from PDB file {}.", pdbId, path);
  Structure s;
  flagLoading(pdbId);
  try {
    PDBFileReader reader = new PDBFileReader(path);
    reader.setFetchBehavior(fetchBehavior);
    reader.setObsoleteBehavior(obsoleteBehavior);
    reader.setFileParsingParameters(params);
    s = reader.getStructureById(pdbId.toLowerCase());
  } finally {
    flagLoadingFinished(pdbId);
  }
  return s;
}

reader.setObsoleteBehavior(cache.getObsoleteBehavior());
reader.setFileParsingParameters(cache.getFileParsingParams());
return reader.getStructure(url);