#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <vector>
#include <map>

// OpenBabel
#include <openbabel/mol.h>
#include <openbabel/residue.h>
#include <openbabel/obconversion.h>

using namespace std;
using namespace OpenBabel;

// 1文字を3文字に変換するための変数設定
map<char, string> aa3;

void init(void) {
  aa3['A'] = "ALA";
  aa3['R'] = "ARG";
  aa3['N'] = "ASN";
  aa3['D'] = "ASP";
  aa3['C'] = "CYS";
  aa3['E'] = "GLU";
  aa3['Q'] = "GLN";
  aa3['G'] = "GLY";
  aa3['H'] = "HIS";
  aa3['I'] = "ILE";
  aa3['L'] = "LEU";
  aa3['K'] = "LYS";
  aa3['M'] = "MET";
  aa3['F'] = "PHE";
  aa3['P'] = "PRO";
  aa3['S'] = "SER";
  aa3['T'] = "THR";
  aa3['W'] = "TRP";
  aa3['Y'] = "TYR";
  aa3['V'] = "VAL";
  aa3['-'] = "GAP";
  aa3['X'] = "ANY";
}

class SEQ {
  string name;
  string seq;
  vector<pair<string, int> > seq3l;
  int pos;

 public:
  SEQ() : pos(0) {}  // コンストラクタ

  SEQ(const SEQ& Obj) {  // コピーコンストラクタ
    name = Obj.name;
    seq = Obj.seq;
    seq3l = Obj.seq3l;
    pos = Obj.pos;
  }

  ~SEQ() {}  // デストラクタ

  bool ReadFASTA(istream* ist) {
    bool _f = false;
    string line;
    pos = 0;

    name.clear();
    while (getline(*ist, line)) {
      if (line[0] == '>') {
        name = line.substr(1);
        _f = true;
        break;
      }
    }
    if (!_f) {
      return false;
    }

    seq.clear();
    streampos spos;
    while (getline(*ist, line)) {
      if (line[0] == '>') {
        break;
      }
      seq = seq + line;
      spos = ist->tellg();
    }
    ist->seekg(spos);

    this->ToTLC();

    return (true);
  }

  void ToTLC(void) {
    seq3l.clear();
    for (int i = 0; i < seq.size(); i++) {
      seq3l.push_back(pair<string, int>(aa3[seq[i]], i + 1));
    }
  }

  string GetName(void) { return name; }

  void SetName(string s) { name = s; }

  int length(void) { return seq.size(); }

  void Reset(void) { pos = 0; }

  char GetChar(int p) {
    if (p > seq.size()) return '\0';
    return seq[p - 1];
  }

  string GetTLC(int p) {
    if (p > seq.size()) return "END";
    return seq3l[p - 1].first;
  }

  pair<string, int> Next(void) {
    if (pos >= seq.size()) return pair<string, int>("END", pos);
    return seq3l[pos++];
  }

  void print_seq(ostream* ost) {
    string x;
    *ost << ">" << name << endl;
    int i = 0;
    for (; i < seq.size() / 60; i++) {
      x = seq.substr(i * 60, 60);
      *ost << x << endl;
    }
    x = seq.substr(i * 60);
    *ost << x << endl;
  }
};

int main(int argc, char* argv[]) {
  // 初期化
  init();
  SEQ s;

  ifstream ifasta("aligned.fasta");
  s.ReadFASTA(&ifasta);
  ifasta.close();

  ifstream ifs("1lke.mol2");
  ofstream ofs("rev_1lke.pdb");

  // フォーマット設定
  OBConversion conv;
  conv.SetInAndOutFormats("MOL2", "PDB");

  // 分子の読み込み
  OBMol mol;
  if (!conv.Read(&mol, &ifs)) {
    cout << "error!" << endl;
    exit(1);
  }

  pair<string, int> tlc;

  s.Reset();
  for (OBResidueIterator rr = mol.BeginResidues(); rr != mol.EndResidues(); rr++) {
    do {
      tlc = s.Next();
    } while (tlc.first == "GAP");
    if (tlc.first == "END") break;

    string r = (*rr)->GetName();
    r=r.substr(0,3); // 最初の3文字を切り出す
    // アミノ酸が一致した場合に番号変更
    if (r == tlc.first) {
      cout << (*rr)->GetName() << "\t" << (*rr)->GetNum();
      cout << " -> " << tlc.second << endl;
      (*rr)->SetNum(tlc.second);  // 番号変更
    }
  }

  conv.Write(&mol, &ofs);
  ofs.close();

  return 0;
}