//  Created by Guillaume GODIN
//  Copyright (C) 2012-2018 Greg Landrum
//   @@ 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 <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/RDLog.h>
#include <vector>
#include <algorithm>
#include <fstream>
#include <string>
#include <sstream>
#include <iterator>
#include <GraphMol/GraphMol.h>
#include <GraphMol/MolOps.h>
#include <boost/tokenizer.hpp>
#include <GraphMol/PeriodicTable.h>
#include <GraphMol/Descriptors/CoulombMat.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <GraphMol/ForceFieldHelpers/MMFF/MMFF.h>
#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>


std::vector<std::string> tokenize(const std::string &s) {
        boost::char_separator<char> sep(", \n\r\t");
        boost::tokenizer<boost::char_separator<char>> tok(s, sep);
        std::vector<std::string> tokens;
        std::copy(tok.begin(), tok.end(), std::back_inserter<std::vector<std::string> >(tokens));
  return tokens;
}



void testCoulombMat1(){
    std::cerr << "===================== Testing CoulombMat  =======================\n";
 
    std::string pathName = getenv("RDBASE");

    // CM test 1
    std::string fNameCM =
         pathName + "/Code/GraphMol/Descriptors/test_data/CM1.out";

    std::string mol_file =
         pathName + "/Code/GraphMol/Descriptors/test_data/bobmol.sdf";

    std::ifstream instrmCM(fNameCM.c_str());
    std::string line;
    std::vector<std::string> tokens; 

    RDKit::ROMOL_SPTR mol( RDKit::MolFileToMol( mol_file , true, false) );


    std::vector<std::vector<double>> Mres;
    int confId = -1;
    RDKit::Descriptors::CoulombMat(*mol, Mres, confId);

    for ( const auto &v : Mres ) {
      std::getline(instrmCM, line);
      tokens = tokenize(line);

      unsigned int ti = 0;
      for ( double x : v )  {
          // std::cout << x << ",";
          TEST_ASSERT(std::fabs(std::stof(tokens[ti]) - x)< 0.001);
          ti++;
      } 
      // std::cout << "\n";
    }
    // std::cout << "\n";
    
    std::cerr << "CM test 1 mat Done\n";
}


int main() {
  RDLog::InitLogs();
  testCoulombMat1();
}