//
//  Copyright (C) 2018 Susan H. Leung
//
//   @@ 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/MolStandardize/TransformCatalog/TransformCatalogParams.h>
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h>
#include "Normalize.h"
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/FileParseException.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/MolStandardize/MolStandardize.h>

#include <fstream>
#include <memory>

using namespace RDKit;
using namespace MolStandardize;

void test1() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n test1" << std::endl;
  std::string smi1, smi2, smi3, smi4, smi5, smi6, smi7;

  Normalizer normalizer;
  auto normalize = [&normalizer](const std::string &smiles) -> std::string {
    std::unique_ptr<ROMol> molecule(SmilesToMol(smiles));
    std::unique_ptr<ROMol> normalized(normalizer.normalize(*molecule));
    return MolToSmiles(*normalized);
  };

  // Test sulfoxide normalization.
  TEST_ASSERT(normalize("CS(C)=O") == "C[S+](C)[O-]");

  // Test sulfone
  TEST_ASSERT(normalize("C[S+2]([O-])([O-])O") == "CS(=O)(=O)O");

  // Test 1,3-separated charges are recombined.
  TEST_ASSERT(normalize("CC([O-])=[N+](C)C") == "CC(=O)N(C)C");

  // Test 1,3-separated charges are recombined.
  TEST_ASSERT(normalize("C[n+]1ccccc1[O-]") == "Cn1ccccc1=O");

  // Test a case where 1,3-separated charges should not be recombined.
  TEST_ASSERT(normalize("CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]") ==
              "CC12CCCCC1(Cl)[N+]([O-])=[N+]2[O-]");

  // Test a case where 1,3-separated charges should not be recombined.
  TEST_ASSERT(normalize("[O-][n+]1cccc[n+]1[O-]") == "[O-][n+]1cccc[n+]1[O-]");

  // Test 1,5-separated charges are recombined.
  TEST_ASSERT(normalize(R"(C[N+](C)=C\C=C\[O-])") == "CN(C)C=CC=O");

  // Test a case where 1,5-separated charges should not be recombined.
  TEST_ASSERT(normalize("C[N+]1=C2C=[N+]([O-])C=CN2CCC1") ==
              "C[N+]1=C2C=[N+]([O-])C=CN2CCC1");

  // Failed on 1k normalize test sanitizeMol step
  TEST_ASSERT(normalize("O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12") ==
              "O=c1cc([O-])[n+](C2OC(CO)C(O)C2O)c2sccn12");

  // Test normalization of 1,3-conjugated cations
  TEST_ASSERT(normalize("C[N+](C)=CN") == "CN(C)C=[NH2+]");
  // verify it doesn't apply to oximes
  TEST_ASSERT(normalize("C[N+](C)=NO") == "C[N+](C)=NO");
  // verify it doesn't affect diazo groups
  TEST_ASSERT(normalize("[N-]=[N+]=CN") == "[N-]=[N+]=CN");
  // but still applies if the adjacent heteroatom is neutral
  TEST_ASSERT(normalize("C[N+](N)=CN") == "CN(N)C=[NH2+]");

  // Test normalization of 1,5-conjugated cations
  TEST_ASSERT(normalize("C[N+](C)=CC=CN") == "CN(C)C=CC=[NH2+]");
  // verify it doesn't apply to oximes
  TEST_ASSERT(normalize("C[N+](C)=CC=NO") == "C[N+](C)=CC=NO");
  // verify it doesn't affect diazo groups
  TEST_ASSERT(normalize("[N-]=[N+]=CC=CN") == "[N-]=[N+]=CC=CN");
  // but still applies if the adjacent heteroatom is neutral
  TEST_ASSERT(normalize("C[N+](N)=CC=CN") == "CN(N)C=CC=[NH2+]");

  // Test normalization of 1,3-conjugated cations
  TEST_ASSERT(normalize("C[N+](C)=c1cccc[nH]1") == "CN(C)c1cccc[nH+]1");
  // verify it doesn't affect diazo groups
  TEST_ASSERT(normalize("[N-]=[N+]=c1cccc[nH]1") == "[N-]=[N+]=c1cccc[nH]1");
  // but still applies if the adjacent heteroatom is neutral
  TEST_ASSERT(normalize("C[N+](N)=c1cccc[nH]1") == "CN(N)c1cccc[nH+]1");

  // Test normalization of 1,5-conjugated cations
  TEST_ASSERT(normalize("C[N+](C)=c1cc[nH]cc1") == "CN(C)c1cc[nH+]cc1");
  // verify it doesn't affect diazo groups
  TEST_ASSERT(normalize("[N-]=[N+]=c1cc[nH]cc1") == "[N-]=[N+]=c1cc[nH]cc1");
  // but still applies if the adjacent heteroatom is neutral
  TEST_ASSERT(normalize("C[N+](N)=c1cc[nH]cc1") == "CN(N)c1cc[nH+]cc1");

  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void test2() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n test2" << std::endl;
  {
    // initialization from string:
    std::string tfdata = R"DATA(//	Name	SMIRKS
Nitro to N+(O-)=O	[N,P,As,Sb;X3:1](=[O,S,Se,Te:2])=[O,S,Se,Te:3]>>[*+1:1]([*-1:2])=[*:3]
Sulfone to S(=O)(=O)	[S+2:1]([O-:2])([O-:3])>>[S+0:1](=[O-0:2])(=[O-0:3])
Pyridine oxide to n+O-	[n:1]=[O:2]>>[n+:1][O-:2]
)DATA";
    std::stringstream sstr(tfdata);
    Normalizer nn(sstr, 10);
    bool debugParse = false;
    bool sanitize = false;
    std::unique_ptr<ROMol> imol(
        SmilesToMol("O=N(=O)CCN=N#N", debugParse, sanitize));
    std::unique_ptr<ROMol> m2(nn.normalize(*imol));
    TEST_ASSERT(MolToSmiles(*m2) == "N#N=NCC[N+](=O)[O-]");
  }
  {
    // initialization from vector:
    std::vector<std::pair<std::string, std::string>> tfdata = {
        {"Nitro to N+(O-)=O",
         "[N,P,As,Sb;X3:1](=[O,S,Se,Te:2])=[O,S,Se,Te:3]>>[*+1:1]([*-1:2])=[*:"
         "3]"},
        {"Sulfone to S(=O)(=O)",
         "[S+2:1]([O-:2])([O-:3])>>[S+0:1](=[O-0:2])(=[O-0:3])"},
        {"Pyridine oxide to n+O-", "[n:1]=[O:2]>>[n+:1][O-:2]"}};
    Normalizer nn(tfdata, 10);
    bool debugParse = false;
    bool sanitize = false;
    std::unique_ptr<ROMol> imol(
        SmilesToMol("O=N(=O)CCN=N#N", debugParse, sanitize));
    std::unique_ptr<ROMol> m2(nn.normalize(*imol));
    TEST_ASSERT(MolToSmiles(*m2) == "N#N=NCC[N+](=O)[O-]");
  }
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testGithub2414() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n Testing github #2414: "
                          "combinatorial explosion in Normalizer"
                       << std::endl;
  // pubchem sid 7638352
  std::string molb = R"MOL(7638352
  -OEChem-01301907472D

143151  0     0  0  0  0  0  0999 V2000
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    2.4646   -6.2630    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7350    2.0001    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3172    0.8272    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9127   -3.0768    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.2298   -4.2734    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.5607    0.3263    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.1090    3.8378    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.3001    1.7525    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.7114   -2.6538    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.7500    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.6154   -0.9002    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9734   -2.1603    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.8297   -7.9562    0.0000 Na  0  0  0  0  0  0  0  0  0  0  0  0
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    3.2849    5.5609    0.0000 Na  0  0  0  0  0  0  0  0  0  0  0  0
    3.9999    3.3368    0.0000 Na  0  0  0  0  0  0  0  0  0  0  0  0
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    6.3019   -1.7415    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.2346    1.4280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6750   -0.5782    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3015   -2.7795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1039   -4.5658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8675    0.4975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.6383    0.4082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6948   -1.9819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END)MOL";

  std::string tfdata = R"DATA(//	Name	SMIRKS
Alkaline oxide to ions	[Li,Na,K;+0:1]-[O+0:2]>>([*+1:1].[O-:2])
)DATA";
  std::stringstream sstr(tfdata);
  Normalizer nn(sstr, 10);
  bool sanitize = false;
  bool removeHs = false;
  std::unique_ptr<ROMol> imol(MolBlockToMol(molb, sanitize, removeHs));
  std::unique_ptr<ROMol> m2(nn.normalize(*imol));
  TEST_ASSERT(m2);
  auto p = "[Na]-O"_smarts;
  TEST_ASSERT(p);
  TEST_ASSERT(SubstructMatch(*imol, *p).size() == 9);
  TEST_ASSERT(SubstructMatch(*m2, *p).size() == 0);
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testNormalizeMultipleAltSmarts() {
  BOOST_LOG(rdInfoLog)
      << "-----------------------\n Testing that multiple SMARTS "
         "matching the same group work"
      << std::endl;
  std::string azideNormalizations = R"DATA(// Name	SMARTS
Azide to N=N+=N-	[N:2]=[N:3]#[N:4]>>[N:2]=[N+:3]=[N-:4]
Broken azide to N=N+=N-	[N:2]=[N:3]=[N:4]>>[NH0:2]=[NH0+:3]=[NH0-:4])DATA";
  std::stringstream azideNormalizationsStream(azideNormalizations);
  std::stringstream captureLog;
  auto ostate = rdInfoLog->df_enabled;
  rdInfoLog->df_enabled = true;
  rdInfoLog->SetTee(captureLog);
  Normalizer nn(azideNormalizationsStream, 200);
  const std::string brokenAzideSmi = "CN=[N+]=[NH-]";
  const int debugParse = 0;
  const bool sanitize = false;
  ROMOL_SPTR brokenAzide(SmilesToMol(brokenAzideSmi, debugParse, sanitize));
  ROMOL_SPTR normalizedAzide(nn.normalize(*brokenAzide));
  rdInfoLog->ClearTee();
  std::string line;
  unsigned int count = 0;
  while (std::getline(captureLog, line)) {
    if (line.find("Rule applied: BrokenazidetoN=N+=N-") != std::string::npos) {
      ++count;
    }
  }
  rdInfoLog->df_enabled = ostate;
  TEST_ASSERT(count == 1);
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testGithub3460() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n Testing Github #3460: "
                          "Normalization rule incorrectly matches sulfones"
                       << std::endl;
  std::stringstream captureLog;
  auto ostate = rdInfoLog->df_enabled;
  rdInfoLog->df_enabled = true;
  rdInfoLog->SetTee(captureLog);
  Normalizer nn;
  auto mol = "[O-][S+]1Nc2c(Cl)cc(Cl)c3c(Cl)cc(Cl)c(c23)N1"_smiles;
  TEST_ASSERT(mol);
  ROMOL_SPTR normalized(nn.normalize(*mol));
  rdInfoLog->ClearTee();
  rdInfoLog->df_enabled = ostate;
  auto logged = captureLog.str();
  TEST_ASSERT(logged.find("Running Normalizer") != std::string::npos);
  TEST_ASSERT(logged.find("Rule applied: C/S+NtoC/S=N+") == std::string::npos);
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testEmptyMol() {
  BOOST_LOG(rdInfoLog) << "-----------------------\n Test that Normalizer "
                          "does not crash on an empty mol"
                       << std::endl;
  Normalizer nn;
  std::unique_ptr<ROMol> emptyMol(new ROMol());
  std::unique_ptr<ROMol> normalized(nn.normalize(*emptyMol));
  TEST_ASSERT(!normalized->getNumAtoms());
}

void testGithub4281() {
  BOOST_LOG(rdInfoLog)
      << "-----------------------\n Testing Github #3460: "
         "Normalization rule incorrectly matches [N+]=O rather than n=O"
      << std::endl;
  auto mol = "Cn1c(=O)c2nc[nH][n+](=O)c2n(C)c1=O"_smiles;
  std::stringstream captureLog;
  rdInfoLog->SetTee(captureLog);
  auto ostate = rdInfoLog->df_enabled;
  rdInfoLog->df_enabled = true;
  Normalizer nn;
  std::unique_ptr<ROMol> normalized(nn.normalize(*mol));
  rdInfoLog->ClearTee();
  rdInfoLog->df_enabled = ostate;
  auto logged = captureLog.str();
  TEST_ASSERT(logged.find("FAILED sanitizeMol") == std::string::npos);
}

int main() {
  RDLog::InitLogs();
  test1();
  test2();
  testGithub2414();
  testNormalizeMultipleAltSmarts();
  testGithub3460();
  testEmptyMol();
  testGithub4281();
  return 0;
}