//  $Id$
// 
//   Copyright (C) 2002-2013 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/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <iostream>

using namespace RDKit;
using namespace std;
typedef class RWMol Mol;


void test1(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test1" << std::endl;
  Mol qM;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0,1,Bond::SINGLE);
  a = new Atom(8);
  m.addAtom(a);
  delete a;
  m.addBond(1,2,Bond::DOUBLE);
  MolOps::sanitizeMol(m);

  QueryAtom *qA = new QueryAtom(6);
  CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(2)),"");
  qA->expandQuery(makeAtomImplicitValenceQuery(3));
  CHECK_INVARIANT(qA->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!qA->Match(m.getAtomWithIdx(2)),"");


  qM.addAtom(qA);
  qA = new QueryAtom(6);
  qA->expandQuery(makeAtomNumQuery(8),Queries::COMPOSITE_OR);
  qM.addAtom(qA);
  qM.addAtom(new QueryAtom(8));
  //Atom::ATOM_SPTR qA(new QueryAtom(6));
  
  QueryBond *qB;
  qB = new QueryBond(Bond::UNSPECIFIED);
  qB->setOwningMol(qM);
  qB->setBeginAtomIdx(0);
  qB->setEndAtomIdx(1);

  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(0)),"");
  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)),"");
  qM.addBond(qB);
  qB = new QueryBond(Bond::DOUBLE);
  qB->setOwningMol(qM);
  qB->setBeginAtomIdx(1);
  qB->setEndAtomIdx(2);
  qM.addBond(qB);


  CHECK_INVARIANT(qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!qM.getAtomWithIdx(0)->Match(m.getAtomWithIdx(2)),"");
  CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(qM.getAtomWithIdx(1)->Match(m.getAtomWithIdx(2)),"");
  CHECK_INVARIANT(!qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(qM.getAtomWithIdx(2)->Match(m.getAtomWithIdx(2)),"");


  CHECK_INVARIANT(qM.getBondWithIdx(0)->Match(m.getBondWithIdx(0)),"");
  CHECK_INVARIANT(qM.getBondWithIdx(0)->Match(m.getBondWithIdx(1)),"");
  CHECK_INVARIANT(!qM.getBondWithIdx(1)->Match(m.getBondWithIdx(0)),"");
  CHECK_INVARIANT(qM.getBondWithIdx(1)->Match(m.getBondWithIdx(1)),"");


  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

void test2(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test2" << std::endl;
  Mol qM;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0,1,Bond::TRIPLE);
  m.addBond(1,2,Bond::SINGLE);
  a = new Atom(8);
  m.addAtom(a);
  delete a;
  m.addBond(2,3,Bond::DOUBLE);
  MolOps::sanitizeMol(m);

  QueryBond *qB;
  qB = new QueryBond(Bond::SINGLE);

  CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(0)),"");
  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)),"");
  CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(2)),"");

  BOND_EQUALS_QUERY *newQ = makeBondOrderEqualsQuery(Bond::DOUBLE);
  qB->expandQuery(newQ,Queries::COMPOSITE_OR);
  CHECK_INVARIANT(!qB->Match(m.getBondWithIdx(0)),"");
  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(1)),"");
  CHECK_INVARIANT(qB->Match(m.getBondWithIdx(2)),"");
  
  
  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}



void test3(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test3" << std::endl;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0,1,Bond::SINGLE);
  m.addBond(1,2,Bond::DOUBLE);
  m.addBond(2,3,Bond::SINGLE);
  m.addBond(3,4,Bond::DOUBLE);
  m.addBond(4,5,Bond::SINGLE);
  m.addBond(5,0,Bond::DOUBLE);
  m.addBond(5,6,Bond::SINGLE);
  MolOps::sanitizeMol(m);
  
  ATOM_EQUALS_QUERY *aeq = makeAtomExplicitDegreeQuery(3);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;
  aeq = makeAtomExplicitDegreeQuery(2);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  aeq = makeAtomHCountQuery(1);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  aeq = makeAtomInNRingsQuery(1);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  aeq = makeAtomInNRingsQuery(0);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  aeq = makeAtomAromaticQuery();
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  aeq = makeAtomAliphaticQuery();
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  aeq = makeAtomInRingQuery();
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
  aeq->setNegation(true);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  aeq = makeAtomInRingOfSizeQuery(6);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
  aeq->setNegation(true);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  aeq = makeAtomInRingOfSizeQuery(5);
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(!aeq->Match(m.getAtomWithIdx(6)),"");
  aeq->setNegation(true);
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;
 
  BOND_EQUALS_QUERY *beq = makeBondIsInRingQuery();
  CHECK_INVARIANT(beq->Match(m.getBondWithIdx(0)),"");
  CHECK_INVARIANT(!beq->Match(m.getBondWithIdx(6)),"");
  CHECK_INVARIANT(beq->Match(m.getBondBetweenAtoms(0,1)),"");
  CHECK_INVARIANT(beq->Match(m.getBondBetweenAtoms(1,0)),"");
  CHECK_INVARIANT(!beq->Match(m.getBondBetweenAtoms(5,6)),"");
  CHECK_INVARIANT(!beq->Match(m.getBondBetweenAtoms(6,5)),"");
  
  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

void test4(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test4" << std::endl;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0,1,Bond::SINGLE);
  m.addBond(1,2,Bond::DOUBLE);
  m.addBond(2,3,Bond::SINGLE);
  m.addBond(3,4,Bond::DOUBLE);
  m.addBond(4,5,Bond::SINGLE);
  m.addBond(5,0,Bond::DOUBLE);
  m.addBond(5,6,Bond::SINGLE);
  MolOps::sanitizeMol(m);
  
  ATOM_NULL_QUERY *aeq = makeAtomNullQuery();
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(0)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(1)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(5)),"");
  CHECK_INVARIANT(aeq->Match(m.getAtomWithIdx(6)),"");
  delete aeq;

  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}


void test5(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test5" << std::endl;
  Mol m;

  Atom *a = new Atom(6);
  // we copy in addAtom, so this is safe
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  m.addAtom(a);
  delete a;
  m.addBond(0,1,Bond::SINGLE);
  m.addBond(1,2,Bond::DOUBLE);
  m.addBond(2,3,Bond::SINGLE);
  m.addBond(3,4,Bond::DOUBLE);
  m.addBond(4,5,Bond::SINGLE);
  m.addBond(5,0,Bond::DOUBLE);
  m.addBond(5,6,Bond::SINGLE);
  MolOps::sanitizeMol(m);
  
  unsigned int valenceProd;
  valenceProd=queryAtomBondProduct(m.getAtomWithIdx(0));
  TEST_ASSERT(valenceProd==1681);  // aromatic*aromatic = 41 * 41 = 1681
  valenceProd=queryAtomBondProduct(m.getAtomWithIdx(1));
  TEST_ASSERT(valenceProd==1681);
  
  valenceProd=queryAtomBondProduct(m.getAtomWithIdx(5));
  TEST_ASSERT(valenceProd==5043);

  valenceProd=queryAtomBondProduct(m.getAtomWithIdx(6));
  TEST_ASSERT(valenceProd==3);
  
  valenceProd=queryAtomAllBondProduct(m.getAtomWithIdx(6));
  TEST_ASSERT(valenceProd==81);
  

  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

void test6(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test6" << std::endl;
  Mol m;

  Atom *a = new Atom(6);
  int massVal;
  massVal=queryAtomMass(a);
  TEST_ASSERT(massVal==static_cast<int>(RDKit::round(12.011*massIntegerConversionFactor)));

  a->setMass(13);
  massVal=queryAtomMass(a);
  TEST_ASSERT(massVal==static_cast<int>(RDKit::round(13.000*massIntegerConversionFactor)));
  
  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

void testQueryQueryMatches(){
  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdInfoLog) << "Testing query--query matches" << std::endl;

  // =====================================
  // ATOMS
  // =====================================
  {
    QueryAtom a1,a2;
    a1.setQuery(makeAtomNullQuery());
    a2.setQuery(makeAtomNullQuery());
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1,a2(6);
    a1.setQuery(makeAtomNullQuery());
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1(6),a2(8);
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1(6),a2(6);
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1,a2;
    a1.setQuery(makeAtomAromaticQuery());
    a2.setQuery(makeAtomAromaticQuery());
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1,a2;
    a1.setQuery(makeAtomAromaticQuery());
    a2.setQuery(makeAtomAliphaticQuery());
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1(6),a2(8);
    a1.expandQuery(makeAtomNumQuery(8),Queries::COMPOSITE_OR);
    a2.expandQuery(makeAtomNumQuery(9),Queries::COMPOSITE_OR);
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1(6),a2(8);
    a1.expandQuery(makeAtomNumQuery(7),Queries::COMPOSITE_OR);
    a2.expandQuery(makeAtomNumQuery(9),Queries::COMPOSITE_OR);
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1(6),a2(6);
    a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
    a2.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1(6),a2(6);
    a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
    a2.expandQuery(makeAtomExplicitValenceQuery(4),Queries::COMPOSITE_AND);
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1(6),a2(8);
    a1.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
    a2.expandQuery(makeAtomExplicitValenceQuery(3),Queries::COMPOSITE_AND);
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryAtom a1(6),a2(8);
    a1.expandQuery(makeAtomNumQuery(8),Queries::COMPOSITE_OR);
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  // =====================================
  // BONDS
  // =====================================
  
  {
    QueryBond a1,a2;
    a1.setQuery(makeBondNullQuery());
    a2.setQuery(makeBondNullQuery());
    TEST_ASSERT(a1.Match(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryBond a1,a2(Bond::SINGLE);
    a1.setQuery(makeBondNullQuery());
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryBond a1(Bond::SINGLE),a2(Bond::SINGLE);
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
    a1.expandQuery(makeBondOrderEqualsQuery(Bond::DOUBLE),Queries::COMPOSITE_OR);
    a2.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
    a1.expandQuery(makeBondOrderEqualsQuery(Bond::TRIPLE),Queries::COMPOSITE_OR);
    a2.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
    a1.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_OR);
    a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_OR);
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  {
    QueryBond a1(Bond::SINGLE),a2(Bond::DOUBLE);
    a1.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
    a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryBond a1(Bond::SINGLE),a2(Bond::SINGLE);
    a1.expandQuery(makeBondMinRingSizeQuery(5),Queries::COMPOSITE_AND);
    a2.expandQuery(makeBondMinRingSizeQuery(4),Queries::COMPOSITE_AND);
    TEST_ASSERT(!a1.QueryMatch(&a2));
    TEST_ASSERT(!a2.QueryMatch(&a1));
  }

  {
    QueryBond a1(Bond::SINGLE),a2(Bond::AROMATIC);
    a1.expandQuery(makeBondOrderEqualsQuery(Bond::AROMATIC),Queries::COMPOSITE_OR);
    TEST_ASSERT(a1.QueryMatch(&a2));
    TEST_ASSERT(a2.QueryMatch(&a1));
  }

  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

void testIssue2892580(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test issue 2892580" << std::endl;
  Mol m;

  Atom *a = new Atom(6);

  int massVal;
  massVal=queryAtomMass(a);
  TEST_ASSERT(massVal==static_cast<int>(RDKit::round(12.011*massIntegerConversionFactor)));

  a->setMass(13);
  massVal=queryAtomMass(a);
  TEST_ASSERT(massVal==static_cast<int>(RDKit::round(13.000*massIntegerConversionFactor)));
  
  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}


void testGithub153(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test github issue 53: query molecules not matching [R]" << std::endl;
  RWMol *m=SmartsToMol("[C]1-[C]-[C]1");
  MolOps::findSSSR(*m);

  RWMol *q=SmartsToMol("[R]");

  std::vector<MatchVectType> mvv;
  TEST_ASSERT(SubstructMatch(*m,*q,mvv));
  TEST_ASSERT(mvv.size()==3);
  TEST_ASSERT(mvv[0].size()==1);
  
  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

void testQualifiedQueries(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test queries using qualifiers instead of ==" << std::endl;
  RWMol *m=SmilesToMol("CNO");

  {
    QueryAtom qA;
    qA.setQuery(makeAtomNumQuery<ATOM_GREATER_QUERY>(7,"test"));
    TEST_ASSERT(qA.Match(m->getAtomWithIdx(0)));
    TEST_ASSERT(!qA.Match(m->getAtomWithIdx(1)));
    TEST_ASSERT(!qA.Match(m->getAtomWithIdx(2)));
  }
  {
    QueryAtom qA;
    qA.setQuery(makeAtomNumQuery<ATOM_GREATEREQUAL_QUERY>(7,"test"));
    TEST_ASSERT(qA.Match(m->getAtomWithIdx(0)));
    TEST_ASSERT(qA.Match(m->getAtomWithIdx(1)));
    TEST_ASSERT(!qA.Match(m->getAtomWithIdx(2)));
  }
  {
    QueryAtom qA;
    qA.setQuery(makeAtomNumQuery<ATOM_LESS_QUERY>(7,"test"));
    TEST_ASSERT(!qA.Match(m->getAtomWithIdx(0)));
    TEST_ASSERT(!qA.Match(m->getAtomWithIdx(1)));
    TEST_ASSERT(qA.Match(m->getAtomWithIdx(2)));
  }
  {
    QueryAtom qA;
    qA.setQuery(makeAtomNumQuery<ATOM_LESSEQUAL_QUERY>(7,"test"));
    TEST_ASSERT(!qA.Match(m->getAtomWithIdx(0)));
    TEST_ASSERT(qA.Match(m->getAtomWithIdx(1)));
    TEST_ASSERT(qA.Match(m->getAtomWithIdx(2)));
  }
  
  delete m;
  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}

void testGithub165(){
  BOOST_LOG(rdErrorLog) << "---------------------- Test Github issue 165: radicals not used in atom-atom matching" << std::endl;

  Atom a1(6);
  Atom a2(6);

  TEST_ASSERT(a1.Match(&a2));
  TEST_ASSERT(a2.Match(&a1));
  a1.setNumRadicalElectrons(2);
  TEST_ASSERT(!a1.Match(&a2));
  TEST_ASSERT(a2.Match(&a1));
  a2.setNumRadicalElectrons(2);
  TEST_ASSERT(a1.Match(&a2));
  TEST_ASSERT(a2.Match(&a1));
  a2.setNumRadicalElectrons(3);
  TEST_ASSERT(!a1.Match(&a2));
  TEST_ASSERT(!a2.Match(&a1));
  
  
  BOOST_LOG(rdErrorLog) << "Done!" << std::endl;
}





int main(){
  RDLog::InitLogs();
  test1();
  test2();
  test3();
  test4();
  test5();
  test6();
  testQueryQueryMatches();
  testIssue2892580();
  testGithub153();
  testQualifiedQueries();
  testGithub165();

  return 0;
}