Program: 16445
Project: 16445
Buggy source:
private void triggerEndFileChecks(){
  currentChain.addGroup(currentGroup);
  currentModel.add(currentChain);
  allModels.add(currentModel);
  assignChainsAndEntities();
  structure.setEntityInfos(entities);
  Date modDate=pdbHeader.getModDate();
  if (modDate.equals(new Date(0))) {
    Date depositionDate=pdbHeader.getDepDate();
    if (!depositionDate.equals(modDate)) {
      pdbHeader.setDepDate(depositionDate);
    }
  }
  structure.setPDBHeader(pdbHeader);
  structure.setCrystallographicInfo(crystallographicInfo);
  if (!journalLines.isEmpty()) {
    buildjournalArticle();
    pdbHeader.setJournalArticle(journalArticle);
  }
  structure.setDBRefs(dbrefs);
  if (params.isAlignSeqRes() && !params.isHeaderOnly()) {
    logger.debug("String_Node_Str");
    SeqRes2AtomAligner aligner=new SeqRes2AtomAligner();
    aligner.align(structure,seqResChains);
  }
 else {
    logger.debug("String_Node_Str");
    SeqRes2AtomAligner.storeUnAlignedSeqRes(structure,seqResChains,params.isHeaderOnly());
  }
  if (!params.isHeaderOnly()) {
    linkSitesToGroups();
  }
  if (bioAssemblyParser != null) {
    pdbHeader.setBioAssemblies(bioAssemblyParser.getTransformationMap());
  }
  if (ncsOperators != null && ncsOperators.size() > 0) {
    crystallographicInfo.setNcsOperators(ncsOperators.toArray(new Matrix4d[ncsOperators.size()]));
  }
  if (rfreeNoCutoffLine > 0 && rfreeStandardLine < 0) {
    pdbHeader.setRfree(rfreeNoCutoffLine);
  }
 else   if (rfreeNoCutoffLine > 0 && rfreeStandardLine > 0) {
    pdbHeader.setRfree(rfreeStandardLine);
  }
 else   if (rfreeNoCutoffLine < 0 && rfreeStandardLine > 0) {
    pdbHeader.setRfree(rfreeStandardLine);
  }
}

Fixed version (ground truth):
private void triggerEndFileChecks(){
  if (currentChain != null && currentGroup != null) {
    currentChain.addGroup(currentGroup);
  }
  if (currentModel != null && currentChain != null) {
    currentModel.add(currentChain);
  }
  if (currentModel != null) {
    allModels.add(currentModel);
  }
  assignChainsAndEntities();
  structure.setEntityInfos(entities);
  Date modDate=pdbHeader.getModDate();
  if (modDate.equals(new Date(0))) {
    Date depositionDate=pdbHeader.getDepDate();
    if (!depositionDate.equals(modDate)) {
      pdbHeader.setDepDate(depositionDate);
    }
  }
  structure.setPDBHeader(pdbHeader);
  structure.setCrystallographicInfo(crystallographicInfo);
  if (!journalLines.isEmpty()) {
    buildjournalArticle();
    pdbHeader.setJournalArticle(journalArticle);
  }
  structure.setDBRefs(dbrefs);
  if (params.isAlignSeqRes() && !params.isHeaderOnly() && !seqResChains.isEmpty()) {
    logger.debug("String_Node_Str");
    SeqRes2AtomAligner aligner=new SeqRes2AtomAligner();
    aligner.align(structure,seqResChains);
  }
 else {
    logger.debug("String_Node_Str");
    SeqRes2AtomAligner.storeUnAlignedSeqRes(structure,seqResChains,params.isHeaderOnly());
  }
  if (!params.isHeaderOnly()) {
    linkSitesToGroups();
  }
  if (bioAssemblyParser != null) {
    pdbHeader.setBioAssemblies(bioAssemblyParser.getTransformationMap());
  }
  if (ncsOperators != null && ncsOperators.size() > 0) {
    crystallographicInfo.setNcsOperators(ncsOperators.toArray(new Matrix4d[ncsOperators.size()]));
  }
  if (rfreeNoCutoffLine > 0 && rfreeStandardLine < 0) {
    pdbHeader.setRfree(rfreeNoCutoffLine);
  }
 else   if (rfreeNoCutoffLine > 0 && rfreeStandardLine > 0) {
    pdbHeader.setRfree(rfreeStandardLine);
  }
 else   if (rfreeNoCutoffLine < 0 && rfreeStandardLine > 0) {
    pdbHeader.setRfree(rfreeStandardLine);
  }
}