// $Id$
//
//  Copyright (C) 2003-2006 Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>

#include <stdlib.h>
#include <iostream>
#include <fstream>
#include <RDGeneral/types.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Substruct/SubstructMatch.h>

using namespace RDKit;

std::string getSmiles(std::string line, std::string &smi) {
  int x = line.find("\t");
  if (x == -1) {
    x = line.find(" ");
  }

  smi = line.substr(0, x);
  std::string rem = line.substr(x + 1, line.length() - x);
  x = rem.find(" ");
  std::string name;
  name = rem.substr(0, x);

  return name;
}

void switchAtoms(RWMol *mol, int idx) {
  ROMol::ADJ_ITER nbrIdx, endNbrs;
  boost::tie(nbrIdx, endNbrs) = mol->getAtomNeighbors(mol->getAtomWithIdx(idx));
  INT_VECT neighs;
  std::map<int, Bond *> nbBnd;
  std::map<int, Bond *>::const_iterator nbi;

  // before removing the atom keep track of the bonds and neighboring atoms
  while (nbrIdx != endNbrs) {
    auto *bnd = new Bond(*(mol->getBondBetweenAtoms(idx, (*nbrIdx))));
    nbBnd[*nbrIdx] = bnd;
    nbrIdx++;
  }

  Atom *oatom = mol->getAtomWithIdx(idx);
  auto *natom = new Atom(*oatom);

  // remove teh aroignal atom
  mol->removeAtom(idx);
  // delete oatom;

  // now add it to the end of the molecule
  int nid = mol->addAtom(natom);

  // then reconnect to the old neighbors with the same bonds we stored
  // keep in mind that if a old neighbor index is greater than that of the
  // removed atom, the id changed by -1

  int nbid;
  for (nbi = nbBnd.begin(); nbi != nbBnd.end(); nbi++) {
    nbid = nbi->first;
    if (nbid > idx) {
      nbid--;
    }
    auto *bnd = new Bond(*(nbi->second));
    bnd->setBeginAtomIdx(nid);
    bnd->setEndAtomIdx(nbid);
    mol->addBond(bnd, true);
  }

  for (nbi = nbBnd.begin(); nbi != nbBnd.end(); nbi++) {
    delete nbi->second;
  }
  nbBnd.clear();
}

void permuteAtoms(RWMol *mol) {
  int nats = mol->getNumAtoms();
  INT_VECT picks;
  INT_VECT_CI pri;
  int i, aid;
  for (i = 0; i < 5; i++) {
    aid = rand() % nats;
    if (std::find(picks.begin(), picks.end(), aid) == picks.end()) {
      picks.push_back(aid);
    }
  }

  for (pri = picks.begin(); pri != picks.end(); pri++) {
    switchAtoms(mol, *pri);
  }
  if (mol->hasProp("SubstructGraphPtr")) mol->clearProp("SubstructGraphPtr");
}

int main(int argc, char *argv[]) {
  RDLog::InitLogs();
  std::string fname;
  if (argc > 1) {
    fname = argv[1];
  } else {
    BOOST_LOG(rdErrorLog) << "Pass in the list of smiles\n";
  }

  std::ifstream inStream(fname.c_str());
  const int MAX_LINE_LEN = 512;
  char inLine[MAX_LINE_LEN];
  std::string tmpstr;
  std::string smi;
  inStream.getline(inLine, MAX_LINE_LEN, '\n');
  tmpstr = inLine;
  // MolOps molop;
  int lineCount = 0;
  while (tmpstr.size() > 0) {
    lineCount++;
    if (!(lineCount % 100)) {
      BOOST_LOG(rdErrorLog) << "Doing: " << lineCount << std::endl;
    }
    if (tmpstr[0] != '#') {
      std::string name = getSmiles(tmpstr, smi);
#ifdef VERBOSE_CANON
      BOOST_LOG(rdInfoLog) << "\n-----------------\nSTART: " << smi
                           << std::endl;
#endif
      // std::cout << " \n";
      RWMol *om = SmilesToMol(smi, 0, 0);
      RWMol *m = SmilesToMol(smi, 0, 0);
      if (m && om) {
        try {
          MolOps::sanitizeMol(*m);
          MolOps::sanitizeMol(*om);
          for (int iter = 0; iter < 5; iter++) {
            std::string preSmi = MolToSmiles(*om);
#if 1
            permuteAtoms(m);
            std::string postSmi = MolToSmiles(*m);
#else
            BOOST_LOG(rdInfoLog) << " ----------------- 2 --------------"
                                 << std::endl;
            std::string postSmi = MolToSmiles(*SmilesToMol(preSmi));
#endif
            std::vector<MatchVectType> fgpMatches;
            int nmat = SubstructMatch(*om, *m, fgpMatches);

            if (preSmi != postSmi) {
              BOOST_LOG(rdInfoLog) << lineCount << " " << name << " " << smi
                                   << " " << preSmi << " " << postSmi
                                   << std::endl;
              iter = 100;
              std::cout << "\n\n";
              m->debugMol(std::cout);
              std::cout << "-*-*-*- MAP -*-*-*-" << std::endl;
              MatchVectType::const_iterator matchI;
              for (matchI = fgpMatches[0].begin();
                   matchI != fgpMatches[0].end(); matchI++) {
                BOOST_LOG(rdInfoLog) << "\t" << matchI->second << "\t"
                                     << matchI->first << std::endl;
              }
              break;
            }

            if (nmat < 1) {
              BOOST_LOG(rdInfoLog) << lineCount << " Not the same mol: " << name
                                   << "\n";
              exit(-1);
            }
          }
          delete om;
          delete m;
        } catch (MolSanitizeException) {
          BOOST_LOG(rdErrorLog) << smi << "\n";
          delete om;
          delete m;
        }
      } else {
        BOOST_LOG(rdErrorLog) << lineCount << " Parse Failed: " << smi
                              << std::endl;
      }
    }
    inStream.getline(inLine, MAX_LINE_LEN, '\n');
    tmpstr = inLine;
  }
  BOOST_LOG(rdErrorLog) << "FINISHED after " << lineCount << " lines."
                        << std::endl;
  return 0;
}