Program: 16351
Project: 16351
Buggy source:
/** 
 * Identify a set of modifications in a a list of chains.
 * @param chains query {@link Chain}s.
 * @param potentialModifications query {@link ProteinModification}s.
 */
public void identify(final List<Chain> chains,final Set<ProteinModification> potentialModifications){
  if (chains == null) {
    throw new IllegalArgumentException("String_Node_Str");
  }
  if (potentialModifications == null) {
    throw new IllegalArgumentException("String_Node_Str");
  }
  reset();
  if (potentialModifications.isEmpty()) {
    return;
  }
  Map<String,Chain> mapChainIdChain=new HashMap<String,Chain>(chains.size());
  residues=new ArrayList<Group>();
  List<Group> ligands=new ArrayList<Group>();
  Map<Component,Set<Group>> mapCompGroups=new HashMap<Component,Set<Group>>();
  for (  Chain chain : chains) {
    mapChainIdChain.put(chain.getChainID(),chain);
    List<Group> ress=StructureUtil.getAminoAcids(chain);
    List<Group> ligs=StructureTools.filterLigands(chain.getAtomGroups());
    residues.addAll(ress);
    residues.removeAll(ligs);
    ligands.addAll(ligs);
    addModificationGroups(potentialModifications,ress,ligs,mapCompGroups);
  }
  if (residues.isEmpty()) {
    String pdbId="String_Node_Str";
    if (chains.size() > 0) {
      Structure struc=chains.get(0).getParent();
      if (struc != null)       pdbId=struc.getPDBCode();
    }
    logger.warn("String_Node_Str",pdbId);
  }
  List<ModifiedCompound> modComps=new ArrayList<ModifiedCompound>();
  for (  ProteinModification mod : potentialModifications) {
    ModificationCondition condition=mod.getCondition();
    List<Component> components=condition.getComponents();
    if (!mapCompGroups.keySet().containsAll(components)) {
      continue;
    }
    int sizeComps=components.size();
    if (sizeComps == 1) {
      processCrosslink1(mapCompGroups,modComps,mod,components);
    }
 else {
      processMultiCrosslink(mapCompGroups,modComps,mod,condition);
    }
  }
  if (recordAdditionalAttachments) {
    for (    ModifiedCompound mc : modComps) {
      identifyAdditionalAttachments(mc,ligands,mapChainIdChain);
    }
  }
  mergeModComps(modComps);
  identifiedModifiedCompounds.addAll(modComps);
  if (recordUnidentifiableModifiedCompounds) {
    recordUnidentifiableAtomLinkages(modComps,ligands);
    recordUnidentifiableModifiedResidues(modComps);
  }
}

Fixed version (ground truth):
/** 
 * Identify a set of modifications in a a list of chains.
 * @param chains query {@link Chain}s.
 * @param potentialModifications query {@link ProteinModification}s.
 */
public void identify(final List<Chain> chains,final Set<ProteinModification> potentialModifications){
  if (chains == null) {
    throw new IllegalArgumentException("String_Node_Str");
  }
  if (potentialModifications == null) {
    throw new IllegalArgumentException("String_Node_Str");
  }
  reset();
  if (potentialModifications.isEmpty()) {
    return;
  }
  residues=new ArrayList<Group>();
  List<Group> ligands=new ArrayList<Group>();
  Map<Component,Set<Group>> mapCompGroups=new HashMap<Component,Set<Group>>();
  for (  Chain chain : chains) {
    List<Group> ress=StructureUtil.getAminoAcids(chain);
    List<Group> ligs=StructureTools.filterLigands(chain.getAtomGroups());
    residues.addAll(ress);
    residues.removeAll(ligs);
    ligands.addAll(ligs);
    addModificationGroups(potentialModifications,ress,ligs,mapCompGroups);
  }
  if (residues.isEmpty()) {
    String pdbId="String_Node_Str";
    if (chains.size() > 0) {
      Structure struc=chains.get(0).getParent();
      if (struc != null)       pdbId=struc.getPDBCode();
    }
    logger.warn("String_Node_Str",pdbId);
  }
  List<ModifiedCompound> modComps=new ArrayList<ModifiedCompound>();
  for (  ProteinModification mod : potentialModifications) {
    ModificationCondition condition=mod.getCondition();
    List<Component> components=condition.getComponents();
    if (!mapCompGroups.keySet().containsAll(components)) {
      continue;
    }
    int sizeComps=components.size();
    if (sizeComps == 1) {
      processCrosslink1(mapCompGroups,modComps,mod,components);
    }
 else {
      processMultiCrosslink(mapCompGroups,modComps,mod,condition);
    }
  }
  if (recordAdditionalAttachments) {
    for (    ModifiedCompound mc : modComps) {
      identifyAdditionalAttachments(mc,ligands,chains);
    }
  }
  mergeModComps(modComps);
  identifiedModifiedCompounds.addAll(modComps);
  if (recordUnidentifiableModifiedCompounds) {
    recordUnidentifiableAtomLinkages(modComps,ligands);
    recordUnidentifiableModifiedResidues(modComps);
  }
}