//
//  Copyright (C) 2002-2017 Greg Landrum and 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 <RDGeneral/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <RDGeneral/RDLog.h>

#include <iostream>
#include <cstdlib>
#include <vector>

using namespace RDKit;
using namespace std;

typedef class ROMol Mol;

void test1() {
  string smi = "CCOC";
  Mol *m = SmilesToMol(smi);
  Mol::AtomIterator atIt;

  unsigned int idx = 0;
  for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) {
    CHECK_INVARIANT((*atIt)->getIdx() == idx, "bad idx");
    idx++;
  }
  atIt = m->beginAtoms();
  CHECK_INVARIANT((*(atIt + 2))->getIdx() == 2, "bad idx");

  atIt = m->beginAtoms();
  Mol::AtomIterator atIt2 = m->beginAtoms();
  CHECK_INVARIANT(atIt == atIt2, "iterators don't compare equal");

  atIt++;
  CHECK_INVARIANT((*atIt)->getIdx() == 1, "bad idx");
  atIt += 2;
  CHECK_INVARIANT((*atIt)->getIdx() == 3, "bad idx");
  atIt -= 1;
  CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");

  CHECK_INVARIANT(atIt != atIt2, "iterators don't compare different");
  CHECK_INVARIANT(atIt2 < atIt, "iterator inequality failed");
  CHECK_INVARIANT(atIt2 <= atIt, "iterator inequality failed");
  CHECK_INVARIANT(atIt > atIt2, "iterator inequality failed");
  CHECK_INVARIANT(atIt >= atIt2, "iterator inequality failed");

  atIt--;
  --atIt;
  CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
  CHECK_INVARIANT(atIt == atIt2, "iterator inequality failed");

  atIt++;
  ++atIt;
  CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");

  atIt = m->beginAtoms();
  atIt = atIt + 2;
  atIt = atIt - 2;
  CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");

  atIt2 = m->beginAtoms();
  atIt2 += 2;
  CHECK_INVARIANT(atIt2 - atIt == 2, "subtraction failed");
  CHECK_INVARIANT(atIt - atIt2 == -2, "subtraction failed");

  // past the end stuff
  atIt2 = m->endAtoms();

  atIt = m->beginAtoms() + 10;
  CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");

  // this is whack
  atIt = m->beginAtoms();
  atIt -= 10;
  CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");

  delete m;
  BOOST_LOG(rdInfoLog) << "test1 done" << endl;
};

void test2() {
  string smi = "C1COC1";
  Mol *m = SmilesToMol(smi);
  Mol::BondIterator bondIt;

  unsigned int idx = 0;
  for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
    CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
    idx++;
  }
  bondIt = m->beginBonds();
  Mol::BondIterator bondIt2 = m->beginBonds();
  CHECK_INVARIANT(bondIt == bondIt2, "iterators don't compare equal");

  bondIt++;
  CHECK_INVARIANT((*bondIt)->getIdx() == 1, "bad idx");
  bondIt++;
  bondIt++;
  bondIt--;
  CHECK_INVARIANT((*bondIt)->getIdx() == 2, "bad idx");

  CHECK_INVARIANT(bondIt != bondIt2, "iterators don't compare different");

  bondIt--;
  --bondIt;
  CHECK_INVARIANT((*bondIt)->getIdx() == 0, "bad idx");
  CHECK_INVARIANT(bondIt == bondIt2, "iterator inequality failed");

  bondIt++;
  ++bondIt;
  CHECK_INVARIANT((*bondIt)->getIdx() == 2, "bad idx");

  // past the end stuff
  bondIt2 = m->endBonds();
  bondIt = m->beginBonds();
  bondIt--;

  delete m;
  BOOST_LOG(rdInfoLog) << "test2 done" << endl;
};

void test3() {
  string smi = "C1COCCNCOCNSCC1";
  unsigned char heteros[] = {2, 5, 7, 9, 10};

  Mol *m = SmilesToMol(smi);
  {
    unsigned int nSeen = 0;
    for (Mol::HeteroatomIterator heteroIt = m->beginHeteros();
         heteroIt != m->endHeteros(); heteroIt++) {
      CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[nSeen], "bad hetero");
      nSeen++;
    }
  }
  {
    unsigned int nSeen = 0;
    for (Mol::HeteroatomIterator heteroIt = m->beginHeteros();
         heteroIt != m->endHeteros(); ++heteroIt) {
      CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[nSeen], "bad hetero");
      nSeen++;
    }
  }
  {
    Mol::HeteroatomIterator heteroIt = m->beginHeteros();
    heteroIt++;
    heteroIt++;
    heteroIt--;
    CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[1], "bad hetero");
    CHECK_INVARIANT((*--heteroIt)->getIdx() == heteros[0], "bad hetero");
    CHECK_INVARIANT((*heteroIt)->getIdx() == heteros[0], "bad hetero");
  }

  delete m;
  BOOST_LOG(rdInfoLog) << "test3 done" << endl;
};

void test4() {
  string smi = "C1COCCNCOCNSCC1";
  unsigned int heteros1[] = {2, 7};

  Mol *m = SmilesToMol(smi);
  auto *q = new QueryAtom();
  q->setQuery(makeAtomNumQuery(8));
  {
    unsigned int nSeen = 0;
    for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
         queryIt != m->endQueryAtoms(); queryIt++) {
      CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[nSeen], "bad query");
      nSeen++;
    }
  }
  {
    Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
    queryIt++;
    queryIt--;
    CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[0], "bad query");
    CHECK_INVARIANT((*++queryIt)->getIdx() == heteros1[1], "bad query");
    CHECK_INVARIANT((*queryIt)->getIdx() == heteros1[1], "bad query");
  }
  {
    Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
    queryIt++;
    queryIt--;
    Mol::QueryAtomIterator queryIt2 = queryIt;
    CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[0], "bad query");
    CHECK_INVARIANT((*++queryIt2)->getIdx() == heteros1[1], "bad query");
    CHECK_INVARIANT((*queryIt2)->getIdx() == heteros1[1], "bad query");
  }
  smi = "CC(C)CC(C)CC(C)CC(C)C";
  unsigned int heteros2[] = {1, 4, 7, 10};

  delete m;
  m = SmilesToMol(smi);
  // m->debugMol(cout);
  q->setQuery(makeAtomImplicitValenceQuery(1));
  {
    unsigned int nSeen = 0;
    for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
         queryIt != m->endQueryAtoms(); ++queryIt) {
      CHECK_INVARIANT((*queryIt)->getIdx() == heteros2[nSeen], "bad query");
      nSeen++;
    }
  }

  delete m;
  delete q;
  BOOST_LOG(rdInfoLog) << "test4 done" << endl;
};

void test5() {
  string smi = "CCCC";
  Mol *m = SmilesToMol(smi);
  Mol::BondIterator bondIt;
  unsigned int idx = 0;
  for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
    CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
    idx++;
  }
  CHECK_INVARIANT(idx == 3, "bad idx");
  idx = 0;
  for (bondIt = m->beginBonds(); bondIt != m->endBonds(); bondIt++) {
    CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
    idx++;
  }
  CHECK_INVARIANT(idx == 3, "bad idx");

  idx = 0;
  Mol::BondIterator beginP(m->beginBonds());
  Mol::BondIterator endP(m->endBonds());
  for (bondIt = beginP; bondIt != endP; bondIt++) {
    CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
    idx++;
  }
  CHECK_INVARIANT(idx == 3, "bad idx");

  delete m;
  BOOST_LOG(rdInfoLog) << "test5 done" << endl;
}

#if 1
void _test6Help(const ROMol *m) {
  Mol::ConstAtomIterator atIt;
  unsigned int idx = 0;
  for (atIt = m->beginAtoms(); atIt != m->endAtoms(); atIt++) {
    CHECK_INVARIANT((*atIt)->getIdx() == idx, "bad idx");
    idx++;
  }
  atIt = m->beginAtoms();
  CHECK_INVARIANT((*(atIt + 2))->getIdx() == 2, "bad idx");

  atIt = m->beginAtoms();
  Mol::ConstAtomIterator atIt2 = m->beginAtoms();
  CHECK_INVARIANT(atIt == atIt2, "iterators don't compare equal");

  atIt++;
  CHECK_INVARIANT((*atIt)->getIdx() == 1, "bad idx");
  atIt += 2;
  CHECK_INVARIANT((*atIt)->getIdx() == 3, "bad idx");
  atIt -= 1;
  CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");

  CHECK_INVARIANT(atIt != atIt2, "iterators don't compare different");
  CHECK_INVARIANT(atIt2 < atIt, "iterator inequality failed");
  CHECK_INVARIANT(atIt2 <= atIt, "iterator inequality failed");
  CHECK_INVARIANT(atIt > atIt2, "iterator inequality failed");
  CHECK_INVARIANT(atIt >= atIt2, "iterator inequality failed");

  atIt--;
  --atIt;
  CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");
  CHECK_INVARIANT(atIt == atIt2, "iterator inequality failed");

  atIt++;
  ++atIt;
  CHECK_INVARIANT((*atIt)->getIdx() == 2, "bad idx");

  atIt = m->beginAtoms();
  atIt = atIt + 2;
  atIt = atIt - 2;
  CHECK_INVARIANT((*atIt)->getIdx() == 0, "bad idx");

  atIt2 = m->beginAtoms();
  atIt2 += 2;
  CHECK_INVARIANT(atIt2 - atIt == 2, "subtraction failed");
  CHECK_INVARIANT(atIt - atIt2 == -2, "subtraction failed");

  // past the end stuff
  atIt2 = m->endAtoms();

  atIt = m->beginAtoms() + 10;
  CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");

  // this is whack
  atIt = m->beginAtoms();
  atIt -= 10;
  CHECK_INVARIANT(atIt >= atIt2, "past-the-end failed");
}
void test6() {
  string smi = "CCOC";
  Mol *m = SmilesToMol(smi);
  _test6Help(m);

  delete m;
  BOOST_LOG(rdInfoLog) << "test6 done" << endl;
};
#endif

void test7() {
  string smi = "c1ccccc1C";
#if 1
  Mol *m = SmilesToMol(smi);
  Mol::AromaticAtomIterator atomIt;
  Mol::AromaticAtomIterator beginP(m->beginAromaticAtoms());
  Mol::AromaticAtomIterator endP(m->endAromaticAtoms());
  unsigned int idx = 0;
  for (atomIt = beginP; atomIt != endP; atomIt++) {
    TEST_ASSERT((*atomIt)->getIdx() == idx);
    idx++;
  }
  TEST_ASSERT(idx == 6);

  atomIt = beginP;
  atomIt++;
  atomIt--;
  TEST_ASSERT((*atomIt)->getIdx() == 0);

  delete m;
  smi = "Cc1ccccc1";
  m = SmilesToMol(smi);
  beginP = m->beginAromaticAtoms();
  endP = m->endAromaticAtoms();
  idx = 0;
  for (atomIt = beginP; atomIt != endP; atomIt++) {
    TEST_ASSERT((*atomIt)->getIdx() == idx + 1);
    idx++;
  }
  TEST_ASSERT(idx == 6);
  delete m;

#endif
  BOOST_LOG(rdInfoLog) << "test7 done" << endl;
}

void testIssue263() {
  string smi = "c1ccccc1C";
#if 1
  Mol *m = SmilesToMol(smi);
  Mol::AtomIterator atomIt;
  unsigned int idx = 0;
  for (atomIt = m->beginAtoms(); atomIt != m->endAtoms(); ++atomIt) {
    TEST_ASSERT((*atomIt)->getIdx() == idx);
    idx++;
  }
  TEST_ASSERT(idx == 7);

  Mol::BondIterator bondIt;
  idx = 0;
  for (bondIt = m->beginBonds(); bondIt != m->endBonds(); ++bondIt) {
    CHECK_INVARIANT((*bondIt)->getIdx() == idx, "bad idx");
    idx++;
  }
  CHECK_INVARIANT(idx == 7, "bad idx");
  delete m;

#endif
  BOOST_LOG(rdInfoLog) << "testIssue263 done" << endl;
}

void test8() {
  {
    string smi = "CC1CC2CC1C2";
    Mol *m = SmilesToMol(smi);
    auto *q = new QueryAtom();
    q->setQuery(makeAtomExplicitDegreeQuery(3));
    q->expandQuery(makeAtomRingBondCountQuery(2));
    unsigned int nSeen = 0;
    for (Mol::QueryAtomIterator queryIt = m->beginQueryAtoms(q);
         queryIt != m->endQueryAtoms(); ++queryIt) {
      TEST_ASSERT((*queryIt)->getIdx() == 1);
      nSeen++;
    }
    TEST_ASSERT(nSeen == 1);
    delete m;
    delete q;
  }

  BOOST_LOG(rdInfoLog) << "test8 done" << endl;
};

int main() {
  RDLog::InitLogs();
  test1();
  test2();
  test3();
  test4();
  test5();
  test6();
  test7();
  test8();
  testIssue263();

  return 0;
}