Program: 17033
Project: 17033
Buggy source:
public void documentEnd(){
  if (current_chain != null) {
    current_chain.addGroup(current_group);
    if (isKnownChain(current_chain.getChainID(),current_model) == null) {
      current_model.add(current_chain);
    }
  }
 else {
    if (DEBUG) {
      System.err.println("String_Node_Str");
    }
  }
  structure.addModel(current_model);
  for (  StructAsym asym : structAsyms) {
    if (DEBUG)     System.out.println("String_Node_Str" + asym.getEntity_id() + "String_Node_Str"+ asym.getId());
    Chain s=getEntityChain(asym.getEntity_id());
    Chain seqres=(Chain)s.clone();
    seqres.setChainID(asym.getId());
    seqResChains.add(seqres);
    if (DEBUG)     System.out.println("String_Node_Str" + asym.getId() + "String_Node_Str"+ seqres+ "String_Node_Str");
  }
  if (params.isAlignSeqRes()) {
    SeqRes2AtomAligner aligner=new SeqRes2AtomAligner();
    aligner.align(structure,seqResChains);
  }
  Set<String> asymIds=asymStrandId.keySet();
  for (int i=0; i < structure.nrModels(); i++) {
    List<Chain> model=structure.getModel(i);
    List<Chain> pdbChains=new ArrayList<Chain>();
    for (    Chain chain : model) {
      for (      String asym : asymIds) {
        if (chain.getChainID().equals(asym)) {
          if (DEBUG)           System.out.println("String_Node_Str" + asym + "String_Node_Str"+ asymStrandId.get(asym));
          chain.setChainID(asymStrandId.get(asym));
          chain.setInternalChainID(asym);
          Chain known=isKnownChain(chain.getChainID(),pdbChains);
          if (known == null) {
            pdbChains.add(chain);
          }
 else {
            for (            Group g : chain.getAtomGroups()) {
              known.addGroup(g);
            }
          }
          break;
        }
      }
    }
    structure.setModel(i,pdbChains);
  }
  PDBHeader header=structure.getPDBHeader();
  header.setNrBioAssemblies(strucAssemblies.size());
  Map<Integer,List<ModelTransformationMatrix>> transformationMap=new HashMap<Integer,List<ModelTransformationMatrix>>();
  int total=strucAssemblies.size();
  for (int i=0; i < total; i++) {
    PdbxStructAssembly psa=strucAssemblies.get(i);
    PdbxStructAssemblyGen psag=strucAssemblyGens.get(i);
    BiologicalAssemblyBuilder builder=new BiologicalAssemblyBuilder();
    List<ModelTransformationMatrix> transformations=builder.getBioUnitTransformationList(psa,psag,structOpers);
    transformationMap.put(i + 1,transformations);
  }
  structure.getPDBHeader().setBioUnitTranformationMap(transformationMap);
}

Fixed version (ground truth):
public void documentEnd(){
  if (current_chain != null) {
    current_chain.addGroup(current_group);
    if (isKnownChain(current_chain.getChainID(),current_model) == null) {
      current_model.add(current_chain);
    }
  }
 else {
    if (DEBUG) {
      System.err.println("String_Node_Str");
    }
  }
  structure.addModel(current_model);
  for (  StructAsym asym : structAsyms) {
    if (DEBUG)     System.out.println("String_Node_Str" + asym.getEntity_id() + "String_Node_Str"+ asym.getId());
    Chain s=getEntityChain(asym.getEntity_id());
    Chain seqres=(Chain)s.clone();
    seqres.setChainID(asym.getId());
    seqResChains.add(seqres);
    if (DEBUG)     System.out.println("String_Node_Str" + asym.getId() + "String_Node_Str"+ seqres+ "String_Node_Str");
  }
  if (params.isAlignSeqRes()) {
    SeqRes2AtomAligner aligner=new SeqRes2AtomAligner();
    aligner.align(structure,seqResChains);
  }
  Set<String> asymIds=asymStrandId.keySet();
  for (int i=0; i < structure.nrModels(); i++) {
    List<Chain> model=structure.getModel(i);
    List<Chain> pdbChains=new ArrayList<Chain>();
    for (    Chain chain : model) {
      for (      String asym : asymIds) {
        if (chain.getChainID().equals(asym)) {
          if (DEBUG)           System.out.println("String_Node_Str" + asym + "String_Node_Str"+ asymStrandId.get(asym));
          chain.setChainID(asymStrandId.get(asym));
          chain.setInternalChainID(asym);
          Chain known=isKnownChain(chain.getChainID(),pdbChains);
          if (known == null) {
            pdbChains.add(chain);
          }
 else {
            for (            Group g : chain.getAtomGroups()) {
              known.addGroup(g);
            }
          }
          break;
        }
      }
    }
    structure.setModel(i,pdbChains);
  }
  PDBHeader header=structure.getPDBHeader();
  header.setNrBioAssemblies(strucAssemblies.size());
  Map<Integer,List<ModelTransformationMatrix>> transformationMap=new HashMap<Integer,List<ModelTransformationMatrix>>();
  int total=strucAssemblies.size();
  System.out.println(total + "String_Node_Str");
  for (int defaultBioAssembly=1; defaultBioAssembly <= total; defaultBioAssembly++) {
    PdbxStructAssembly psa=strucAssemblies.get(defaultBioAssembly - 1);
    List<PdbxStructAssemblyGen> psags=new ArrayList<PdbxStructAssemblyGen>(1);
    for (    PdbxStructAssemblyGen psag : strucAssemblyGens) {
      if (psag.getAssembly_id().equals(defaultBioAssembly + "String_Node_Str")) {
        psags.add(psag);
      }
    }
    BiologicalAssemblyBuilder builder=new BiologicalAssemblyBuilder();
    List<ModelTransformationMatrix> transformations=builder.getBioUnitTransformationList(psa,psags,structOpers);
    transformationMap.put(defaultBioAssembly,transformations);
  }
  structure.getPDBHeader().setBioUnitTranformationMap(transformationMap);
}