code: public static AtomCache setUpBioJava() {
  		// Set up the atom cache etc
  		AtomCache cache = new AtomCache();
  		cache.setUseMmCif(true);
  		FileParsingParameters params = cache.getFileParsingParams();
  		params.setCreateAtomBonds(true);
  		params.setAlignSeqRes(true);
  		params.setParseBioAssembly(true);
  		DownloadChemCompProvider cc = new DownloadChemCompProvider();
  		ChemCompGroupFactory.setChemCompProvider(cc);
  		cc.checkDoFirstInstall();
  		cache.setFileParsingParams(params);
  		StructureIO.setAtomCache(cache);
  		return cache;
  	}
docs: Set up the configuration parameters for BioJava.