/**
   * identify additional groups that are not directly attached to amino acids.
   *
   * @param mc {@link ModifiedCompound}.
   * @param chain a {@link Chain}.
   * @return a list of added groups.
   */
  private void identifyAdditionalAttachments(
      ModifiedCompound mc, List<Group> ligands, Map<String, Chain> mapChainIdChain) {
    if (ligands.isEmpty()) {
      return;
    }

    // TODO: should the additional groups only be allowed to the identified
    // ligands or both amino acids and ligands? Currently only on ligands
    // ligands to amino acid bonds for same modification of unknown category
    // will be combined in mergeModComps()
    // TODO: how about chain-chain links?
    List<Group> identifiedGroups = new ArrayList<Group>();
    for (StructureGroup num : mc.getGroups(false)) {
      Group group;
      try {
        // String numIns = "" + num.getResidueNumber();
        // if (num.getInsCode() != null) {
        //	numIns += num.getInsCode();
        // }
        ResidueNumber resNum = new ResidueNumber();
        resNum.setChainId(num.getChainId());
        resNum.setSeqNum(num.getResidueNumber());
        resNum.setInsCode(num.getInsCode());
        // group = chain.getGroupByPDB(numIns);
        group = mapChainIdChain.get(num.getChainId()).getGroupByPDB(resNum);
      } catch (StructureException e) {
        e.printStackTrace();
        // should not happen
        continue;
      }
      identifiedGroups.add(group);
    }

    int start = 0;

    int n = identifiedGroups.size();
    while (n > start) {
      for (Group group1 : ligands) {
        for (int i = start; i < n; i++) {
          Group group2 = identifiedGroups.get(i);
          if (!identifiedGroups.contains(group1)) {
            List<Atom[]> linkedAtoms =
                StructureUtil.findAtomLinkages(group1, group2, false, bondLengthTolerance);
            if (!linkedAtoms.isEmpty()) {
              for (Atom[] atoms : linkedAtoms) {
                mc.addAtomLinkage(
                    StructureUtil.getStructureAtomLinkage(atoms[0], false, atoms[1], false));
              }
              identifiedGroups.add(group1);
              break;
            }
          }
        }
      }

      start = n;
      n = identifiedGroups.size();
    }
  }
  /**
   * Record unidentifiable atom linkages in a chain. Only linkages between two residues or one
   * residue and one ligand will be recorded.
   */
  private void recordUnidentifiableAtomLinkages(
      List<ModifiedCompound> modComps, List<Group> ligands) {

    // first put identified linkages in a map for fast query
    Set<StructureAtomLinkage> identifiedLinkages = new HashSet<StructureAtomLinkage>();
    for (ModifiedCompound mc : modComps) {
      identifiedLinkages.addAll(mc.getAtomLinkages());
    }

    // record
    // cross link
    int nRes = residues.size();
    for (int i = 0; i < nRes - 1; i++) {
      Group group1 = residues.get(i);
      for (int j = i + 1; j < nRes; j++) {
        Group group2 = residues.get(j);
        List<Atom[]> linkages =
            StructureUtil.findAtomLinkages(group1, group2, true, bondLengthTolerance);
        for (Atom[] atoms : linkages) {
          StructureAtomLinkage link =
              StructureUtil.getStructureAtomLinkage(atoms[0], true, atoms[1], true);
          unidentifiableAtomLinkages.add(link);
        }
      }
    }

    // attachment
    int nLig = ligands.size();
    for (int i = 0; i < nRes; i++) {
      Group group1 = residues.get(i);
      for (int j = 0; j < nLig; j++) {
        Group group2 = ligands.get(j);
        if (group1.equals(group2)) { // overlap between residues and ligands
          continue;
        }
        List<Atom[]> linkages =
            StructureUtil.findAtomLinkages(group1, group2, false, bondLengthTolerance);
        for (Atom[] atoms : linkages) {
          StructureAtomLinkage link =
              StructureUtil.getStructureAtomLinkage(atoms[0], true, atoms[1], false);
          unidentifiableAtomLinkages.add(link);
        }
      }
    }
  }
  /**
   * Assembly the matched linkages.
   *
   * @param matchedAtomsOfLinkages
   * @param mod
   * @param condition
   * @param ret ModifiedCompound will be stored here.
   */
  private void assembleLinkages(
      List<List<Atom[]>> matchedAtomsOfLinkages,
      ProteinModification mod,
      List<ModifiedCompound> ret) {
    ModificationCondition condition = mod.getCondition();
    List<ModificationLinkage> modLinks = condition.getLinkages();

    int nLink = matchedAtomsOfLinkages.size();
    int[] indices = new int[nLink];
    Set<ModifiedCompound> identifiedCompounds = new HashSet<ModifiedCompound>();
    while (indices[0] < matchedAtomsOfLinkages.get(0).size()) {
      List<Atom[]> atomLinkages = new ArrayList<Atom[]>(nLink);
      for (int iLink = 0; iLink < nLink; iLink++) {
        Atom[] atoms = matchedAtomsOfLinkages.get(iLink).get(indices[iLink]);
        atomLinkages.add(atoms);
      }
      if (matchLinkages(modLinks, atomLinkages)) {
        // matched

        int n = atomLinkages.size();
        List<StructureAtomLinkage> linkages = new ArrayList<StructureAtomLinkage>(n);
        for (int i = 0; i < n; i++) {
          Atom[] linkage = atomLinkages.get(i);
          StructureAtomLinkage link =
              StructureUtil.getStructureAtomLinkage(
                  linkage[0], residues.contains(linkage[0].getGroup()),
                  linkage[1], residues.contains(linkage[1].getGroup()));
          linkages.add(link);
        }

        ModifiedCompound mc = new ModifiedCompoundImpl(mod, linkages);
        if (!identifiedCompounds.contains(mc)) {
          ret.add(mc);
          identifiedCompounds.add(mc);
        }
      }

      // indices++ (e.g. [0,0,1]=>[0,0,2]=>[1,2,0])
      int i = nLink - 1;
      while (i >= 0) {
        if (i == 0 || indices[i] < matchedAtomsOfLinkages.get(i).size() - 1) {
          indices[i]++;
          break;
        } else {
          indices[i] = 0;
          i--;
        }
      }
    }
  }
  private void recordUnidentifiableModifiedResidues(List<ModifiedCompound> modComps) {
    Set<StructureGroup> identifiedComps = new HashSet<StructureGroup>();
    for (ModifiedCompound mc : modComps) {
      identifiedComps.addAll(mc.getGroups(true));
    }

    // TODO: use the ModifiedAminoAcid after Andreas add that.
    for (Group group : residues) {
      if (group.getType().equals(GroupType.HETATM)) {
        StructureGroup strucGroup = StructureUtil.getStructureGroup(group, true);
        if (!identifiedComps.contains(strucGroup)) {
          unidentifiableModifiedResidues.add(strucGroup);
        }
      }
    }
  }
 private void processCrosslink1(
     Map<Component, Set<Group>> mapCompGroups,
     List<ModifiedCompound> modComps,
     ProteinModification mod,
     List<Component> components) {
   // modified residue
   // TODO: is this the correct logic for CROSS_LINK_1?
   Set<Group> modifiedResidues = mapCompGroups.get(components.get(0));
   if (modifiedResidues != null) {
     for (Group residue : modifiedResidues) {
       StructureGroup strucGroup = StructureUtil.getStructureGroup(residue, true);
       ModifiedCompound modRes = new ModifiedCompoundImpl(mod, strucGroup);
       modComps.add(modRes);
     }
   }
 }
  /** Get matched atoms for all linkages. */
  private List<List<Atom[]>> getMatchedAtomsOfLinkages(
      ModificationCondition condition, Map<Component, Set<Group>> mapCompGroups) {
    List<ModificationLinkage> linkages = condition.getLinkages();
    int nLink = linkages.size();

    List<List<Atom[]>> matchedAtomsOfLinkages = new ArrayList<List<Atom[]>>(nLink);

    for (int iLink = 0; iLink < nLink; iLink++) {
      ModificationLinkage linkage = linkages.get(iLink);
      Component comp1 = linkage.getComponent1();
      Component comp2 = linkage.getComponent2();

      //			boolean isAA1 = comp1.;
      //			boolean isAA2 = comp2.getType()==true;

      Set<Group> groups1 = mapCompGroups.get(comp1);
      Set<Group> groups2 = mapCompGroups.get(comp2);

      List<Atom[]> list = new ArrayList<Atom[]>();

      List<String> potentialNamesOfAtomOnGroup1 = linkage.getPDBNameOfPotentialAtomsOnComponent1();
      for (String name : potentialNamesOfAtomOnGroup1) {
        if (name.equals("*")) {
          // wildcard
          potentialNamesOfAtomOnGroup1 = null; // search all atoms
          break;
        }
      }

      List<String> potentialNamesOfAtomOnGroup2 = linkage.getPDBNameOfPotentialAtomsOnComponent2();
      for (String name : potentialNamesOfAtomOnGroup2) {
        if (name.equals("*")) {
          // wildcard
          potentialNamesOfAtomOnGroup2 = null; // search all atoms
          break;
        }
      }

      for (Group g1 : groups1) {
        for (Group g2 : groups2) {
          if (g1.equals(g2)) {
            continue;
          }

          // only for wildcard match of two residues
          boolean ignoreNCLinkage =
              potentialNamesOfAtomOnGroup1 == null
                  && potentialNamesOfAtomOnGroup2 == null
                  && residues.contains(g1)
                  && residues.contains(g2);

          Atom[] atoms =
              StructureUtil.findNearestAtomLinkage(
                  g1,
                  g2,
                  potentialNamesOfAtomOnGroup1,
                  potentialNamesOfAtomOnGroup2,
                  ignoreNCLinkage,
                  bondLengthTolerance);
          if (atoms != null) {
            list.add(atoms);
          }
        }
      }

      if (list.isEmpty()) {
        // broken linkage
        break;
      }

      matchedAtomsOfLinkages.add(list);
    }

    return matchedAtomsOfLinkages;
  }
  /**
   * 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("Null structure.");
    }

    if (potentialModifications == null) {
      throw new IllegalArgumentException("Null potentialModifications.");
    }

    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 = chain.getAtomLigands();
      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 = "?";
      if (chains.size() > 0) {
        Structure struc = chains.get(0).getParent();
        if (struc != null) pdbId = struc.getPDBCode();
      }
      System.err.println(
          "WARNING: no amino acids found for "
              + pdbId
              + ". Either you did not parse the PDB file with alignSEQRES records, or this record does not contain any amino acids.");
    }
    List<ModifiedCompound> modComps = new ArrayList<ModifiedCompound>();

    for (ProteinModification mod : potentialModifications) {
      ModificationCondition condition = mod.getCondition();
      List<Component> components = condition.getComponents();
      if (!mapCompGroups.keySet().containsAll(components)) {
        // not all components exist for this mod.
        continue;
      }

      int sizeComps = components.size();
      if (sizeComps == 1) {

        processCrosslink1(mapCompGroups, modComps, mod, components);

      } else {

        processMultiCrosslink(mapCompGroups, modComps, mod, condition);
      }
    }

    if (recordAdditionalAttachments) {
      // identify additional groups that are not directly attached to amino acids.
      for (ModifiedCompound mc : modComps) {
        identifyAdditionalAttachments(mc, ligands, mapChainIdChain);
      }
    }

    mergeModComps(modComps);

    identifiedModifiedCompounds.addAll(modComps);

    // record unidentifiable linkage
    if (recordUnidentifiableModifiedCompounds) {
      recordUnidentifiableAtomLinkages(modComps, ligands);
      recordUnidentifiableModifiedResidues(modComps);
    }
  }