//
//  Copyright (C) 2003-2015 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 <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/SmilesParse/SmilesParse.h>


#include <iostream>
using namespace std;
using namespace RDKit;

void test1(){
  Atom *a1 = new Atom(6);
  Atom *a2 = new Atom(*a1);
  Atom *a3 = a1->copy();
  delete a1;
  delete a2;
  delete a3;

}

void test2(){
  RWMol *mol = new RWMol();

  mol->addAtom(new Atom(6));
  mol->addAtom(new Atom(6));
  mol->addAtom(new Atom(8));
  mol->addBond(0,1,Bond::SINGLE);
  mol->addBond(1,2,Bond::SINGLE);
  mol->setAtomBookmark(mol->getAtomWithIdx(1),1);
  mol->setBondBookmark(mol->getBondWithIdx(0),2);
  CHECK_INVARIANT(mol->hasAtomBookmark(1),"");
  CHECK_INVARIANT(mol->getAtomWithBookmark(1)->getIdx()==1,"");
  CHECK_INVARIANT(mol->hasBondBookmark(2),"");
  CHECK_INVARIANT(mol->getBondWithBookmark(2)->getIdx()==0,"");

  RWMol *mol2 = new RWMol(*mol);
  CHECK_INVARIANT(mol2->hasAtomBookmark(1),"");
  CHECK_INVARIANT(mol2->getAtomWithBookmark(1)->getIdx()==1,"");
  CHECK_INVARIANT(mol2->hasBondBookmark(2),"");
  CHECK_INVARIANT(mol2->getBondWithBookmark(2)->getIdx()==0,"");

}

void testQueryCopying()
{
  BOOST_LOG(rdInfoLog) << "-----------------------\n Testing behavior of copied queries" << std::endl;

  {
    std::string smi="[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),$([nH0,o,s;+0])]";
    ROMol *m=static_cast<ROMol *>(SmartsToMol(smi));
    TEST_ASSERT(m);
    std::cerr<<"\n\n\nCOPY"<<std::endl;
    ROMol *m2 = new ROMol(*m,true);
    
    delete m;
    delete m2;
  }
  
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

void testConformerCopying()
{
  BOOST_LOG(rdInfoLog) << "-----------------------\n Testing copying conformers" << std::endl;

  {
    std::string smi="CCC";
    ROMol *m=static_cast<ROMol *>(SmilesToMol(smi));
    TEST_ASSERT(m);

    Conformer *conf=new Conformer(m->getNumAtoms());
    conf->setId(1);
    m->addConformer(conf,false);
    conf=new Conformer(m->getNumAtoms());
    conf->setId(2);
    m->addConformer(conf,false);
    {
      ROMol *m2 = new ROMol(*m);
      TEST_ASSERT(m2->getNumConformers()==2);
      delete m2;
    }
    {
      ROMol *m2 = new ROMol(*m,false,1);
      TEST_ASSERT(m2->getNumConformers()==1);
      TEST_ASSERT(m2->getConformer().getId()==1);
      delete m2;
    }
    {
      ROMol *m2 = new ROMol(*m,false,2);
      TEST_ASSERT(m2->getNumConformers()==1);
      TEST_ASSERT(m2->getConformer().getId()==2);
      delete m2;
    }
    {
      ROMol *m2 = new ROMol(*m,false,3);
      TEST_ASSERT(m2->getNumConformers()==0);
      delete m2;
    }

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




// -------------------------------------------------------------------
int main()
{
#if 0
  test1();
  test2();
#endif
  testQueryCopying();
  testConformerCopying();
  return 0;
}