//
//  Copyright (C) 2014 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 <GraphMol/new_canon.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/hanoiSort.h>

#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>

#include <iostream>
#include <vector>
#include <boost/random.hpp>
#include <cstdlib>

using namespace RDKit;


int pcmp(const void *a,const void *b){
  if((*(int *)a)<(*(int *)b)){
    return -1;
  } else if((*(int *)a)>(*(int *)b)){
    return 1;
  }
  return 0;
}
int icmp(int a,int b){
  if(a<b){
    return -1;
  } else if(a>b){
    return 1;
  }
  return 0;
}

class int_compare_ftor {
  const int *dp_ints;
public:
  int_compare_ftor() : dp_ints(NULL) {};
  int_compare_ftor(const int *ints) : dp_ints(ints) {};
  int operator()(int i,int j) const {
    PRECONDITION(dp_ints,"no ints");
    unsigned int ivi= dp_ints[i];
    unsigned int ivj= dp_ints[j];
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;
    else
      return 0;
  }
};

void qs1(  const std::vector< std::vector<int> > &vects){
  BOOST_LOG(rdInfoLog)<<"sorting (qsort) vectors"<<std::endl;
  for(unsigned int i=0;i<vects.size();++i){
    std::vector<int> tv=vects[i];
    int *data=&tv.front();
    qsort(data,tv.size(),sizeof(int),pcmp);
    for(unsigned int j=1;j<tv.size();++j){
      TEST_ASSERT(tv[j]>=tv[j-1]);
    }
  }
  BOOST_LOG(rdInfoLog)<< "done: " << vects.size()<<std::endl;
}

void hs1(  const std::vector< std::vector<int> > &vects){
  BOOST_LOG(rdInfoLog)<<"sorting (hanoi sort) vectors"<<std::endl;
  for(unsigned int i=0;i<vects.size();++i){
    const int *data=&vects[i].front();
    int_compare_ftor icmp(data);
    int *indices=(int *)malloc(vects[i].size()*sizeof(int));
    for(unsigned int j=0;j<vects[i].size();++j) indices[j]=j;
    int *count=(int *)malloc(vects[i].size()*sizeof(int));
    int *changed=(int *)malloc(vects[i].size()*sizeof(int));
    memset(changed, 1, vects[i].size()*sizeof(int));
    RDKit::hanoisort(indices,vects[i].size(),count,changed,icmp);
    for(unsigned int j=1;j<vects[i].size();++j){
      TEST_ASSERT(data[indices[j]]>=data[indices[j-1]]);
    }
    free(count);
    free(indices);
  }
  BOOST_LOG(rdInfoLog)<< "done: " << vects.size()<<std::endl;
}

void test1(){
  BOOST_LOG(rdInfoLog) << "Testing the hanoi sort" << std::endl;

  typedef boost::random::mersenne_twister<boost::uint32_t,32,4,2,31,0x9908b0df,11,7,0x9d2c5680,15,0xefc60000,18, 3346425566U>  rng_type;
  typedef boost::uniform_int<> distrib_type;
  typedef boost::variate_generator<rng_type &,distrib_type> source_type;
  rng_type generator(42u);

  const unsigned int nVects=500000;
  const unsigned int vectSize=50;
  const unsigned int nClasses=15;

  distrib_type dist(0,nClasses);
  source_type randomSource(generator,dist);

  BOOST_LOG(rdInfoLog)<<"populating vectors"<<std::endl;
  std::vector< std::vector<int> > vects(nVects);
  for(unsigned int i=0;i<nVects;++i){
    vects[i] = std::vector<int>(vectSize);
    for(unsigned int j=0;j<vectSize;++j){
      vects[i][j] = randomSource();
    }
  }

  //qs1(vects);
  hs1(vects);
  BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};


class atomcomparefunctor {
  Canon::canon_atom *d_atoms;
public:
  atomcomparefunctor() : d_atoms(NULL) {};
  atomcomparefunctor(Canon::canon_atom *atoms) : d_atoms(atoms) {};
  int operator()(int i,int j) const {
    PRECONDITION(d_atoms,"no atoms");
    unsigned int ivi,ivj;

    // always start with the current class:
    ivi= d_atoms[i].index;
    ivj= d_atoms[j].index;
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;

    ivi= d_atoms[i].atom->getAtomicNum();
    ivj= d_atoms[j].atom->getAtomicNum();
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;

    return 0;
  }
};
class atomcomparefunctor2 {
  Canon::canon_atom *d_atoms;
public:
  atomcomparefunctor2() : d_atoms(NULL) {};
  atomcomparefunctor2(Canon::canon_atom *atoms) : d_atoms(atoms) {};
  int operator()(int i,int j) const {
    PRECONDITION(d_atoms,"no atoms");
    unsigned int ivi,ivj;

    // always start with the current class:
    ivi= d_atoms[i].index;
    ivj= d_atoms[j].index;
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;

    // start by comparing degree
    ivi= d_atoms[i].atom->getDegree();
    ivj= d_atoms[j].atom->getDegree();
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;

    // move onto atomic number
    ivi= d_atoms[i].atom->getAtomicNum();
    ivj= d_atoms[j].atom->getAtomicNum();
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;

    return 0;
  }
};

void test2(){
  BOOST_LOG(rdInfoLog) << "Testing hanoi with a functor." << std::endl;
  // make sure that hanoi works with a functor and "molecule data"
  {
    std::string smi="FC1C(Cl)C1C";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);
    std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
    std::vector<int> indices(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      atoms[i].atom = m->getAtomWithIdx(i);
      atoms[i].index=0;
      indices[i]=i;
    }
    atomcomparefunctor ftor(&atoms.front());

    int *data=&indices.front();
    int *count=(int *)malloc(atoms.size()*sizeof(int));
    int *changed=(int *)malloc(atoms.size()*sizeof(int));
    memset(changed, 1, atoms.size()*sizeof(int));
    RDKit::hanoisort(data,atoms.size(),count,changed,ftor);

    for(unsigned int i=0;i<m->getNumAtoms();++i){
      //std::cerr<<indices[i]<<" "<<" index: "<<atoms[indices[i]].index<<" count: "<<count[indices[i]]<<std::endl;
      if(i>0){
        TEST_ASSERT(atoms[indices[i]].atom->getAtomicNum() >= atoms[indices[i-1]].atom->getAtomicNum());
        if(atoms[indices[i]].atom->getAtomicNum() != atoms[indices[i-1]].atom->getAtomicNum()){
          TEST_ASSERT(count[indices[i]]!=0);
        } else {
          TEST_ASSERT(count[indices[i]]==0);
        }
      } else {
        TEST_ASSERT(count[indices[i]]!=0);
      }
    }
  }
  BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};

void test3(){
  BOOST_LOG(rdInfoLog) << "Testing basic partition refinement." << std::endl;
  // basic partition refinement
  {
    std::string smi="FC1C(Cl)CCC1C";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);
    std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
    initCanonAtoms(*m,atoms,true);
    atomcomparefunctor ftor(&atoms.front());

    RDKit::Canon::canon_atom *data=&atoms.front();
    int *count=(int *)malloc(atoms.size()*sizeof(int));
    int *order=(int *)malloc(atoms.size()*sizeof(int));
    int activeset;
    int *next=(int *)malloc(atoms.size()*sizeof(int));
    int *changed=(int *)malloc(atoms.size()*sizeof(int));
    memset(changed, 1, atoms.size()*sizeof(int));
    char *touched=(char *)malloc(atoms.size()*sizeof(char));

    RDKit::Canon::CreateSinglePartition(atoms.size(),order,count,data);
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);


    // std::cerr<<"----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //   std::cerr<<i<<" "<<atoms[i].index<<" "<<count[i]<<" "<<next[i]<<" "<<order[i]<<std::endl;
    // }

    RDKit::Canon::RefinePartitions(*m,data,ftor,false,order,count,activeset,next,changed,touched);

    // std::cerr<<"----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //   std::cerr<<i<<" "<<atoms[i].index<<" "<<count[i]<<" "<<next[i]<<" "<<order[i]<<std::endl;
    // }

    // std::cerr<<"----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //   std::cerr<<order[i]<<" "<<atoms[order[i]].invar<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
    // }

    TEST_ASSERT(order[0]==1);
    TEST_ASSERT(order[6]==0);
    TEST_ASSERT(order[7]==3);
    TEST_ASSERT(count[order[0]]==6);
    TEST_ASSERT(count[order[1]]==0);
    TEST_ASSERT(count[order[6]]==1);
    TEST_ASSERT(count[order[7]]==1);
  }
  {
    // this time with smarter invariants
    std::string smi="FC1C(Cl)CCC1C";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);
    std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
    initCanonAtoms(*m,atoms,true);
    atomcomparefunctor2 ftor(&atoms.front());

    RDKit::Canon::canon_atom *data=&atoms.front();
    int *count=(int *)malloc(atoms.size()*sizeof(int));
    int *order=(int *)malloc(atoms.size()*sizeof(int));
    int activeset;
    int *next=(int *)malloc(atoms.size()*sizeof(int));
    int *changed=(int *)malloc(atoms.size()*sizeof(int));
    memset(changed, 1, atoms.size()*sizeof(int));
    char *touched=(char *)malloc(atoms.size()*sizeof(char));
    
    RDKit::Canon::CreateSinglePartition(atoms.size(),order,count,data);
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);

    RDKit::Canon::RefinePartitions(*m,data,ftor,false,order,count,activeset,next,changed,touched);

    // std::cerr<<"----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //   std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
    // }

    TEST_ASSERT(order[0]==7);
    TEST_ASSERT(order[1]==0);
    TEST_ASSERT(order[2]==3);
    TEST_ASSERT(order[3]==4);
    TEST_ASSERT(order[5]==1);
    TEST_ASSERT(count[order[0]]==1);
    TEST_ASSERT(count[order[1]]==1);
    TEST_ASSERT(count[order[2]]==1);
    TEST_ASSERT(count[order[3]]==2);
    TEST_ASSERT(count[order[4]]==0);
    TEST_ASSERT(count[order[5]]==3);
    TEST_ASSERT(count[order[6]]==0);

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


class atomcomparefunctor3 {
  Canon::canon_atom *dp_atoms;
  const ROMol *dp_mol;
  unsigned int getAtomNeighborhood(unsigned int i) const{
    unsigned int res=0;
    const Atom *at=dp_mol->getAtomWithIdx(i);
    std::vector<unsigned int> nbrs(at->getDegree());
    unsigned int nbridx=0;
    ROMol::OEDGE_ITER beg,end;
    boost::tie(beg,end) = dp_mol->getAtomBonds(at);
    while(beg!=end){
      const BOND_SPTR bond=(*dp_mol)[*beg];
      nbrs[nbridx]=static_cast<unsigned int>(100*bond->getBondTypeAsDouble())+dp_atoms[bond->getOtherAtomIdx(i)].index;
      ++beg;
      ++nbridx;
    }
    std::sort(nbrs.begin(),nbrs.end());
    for(nbridx=0;nbridx<at->getDegree();++nbridx){
      res+=(nbridx+1)*1000+nbrs[nbridx];
    }
    return res;
  }
  int basecomp(int i,int j) const {
    PRECONDITION(dp_atoms,"no atoms");
    unsigned int ivi,ivj;

    // always start with the current class:
    ivi= dp_atoms[i].index;
    ivj= dp_atoms[j].index;
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;
    
    // start by comparing degree
    ivi= dp_atoms[i].atom->getDegree();
    ivj= dp_atoms[j].atom->getDegree();
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;

    // move onto atomic number
    ivi= dp_atoms[i].atom->getAtomicNum();
    ivj= dp_atoms[j].atom->getAtomicNum();
    if(ivi<ivj)
      return -1;
    else if(ivi>ivj)
      return 1;

    return 0;
  }
public:
  bool df_useNbrs;
  atomcomparefunctor3() : dp_atoms(NULL), dp_mol(NULL), df_useNbrs(false) {};
  atomcomparefunctor3(Canon::canon_atom *atoms, const ROMol &m) : dp_atoms(atoms), dp_mol(&m),
                                                                  df_useNbrs(false) {};
  int operator()(int i,int j) const {
    PRECONDITION(dp_atoms,"no atoms");
    PRECONDITION(dp_mol,"no molecule");
    int v=basecomp(i,j);
    if(v) return v;
    unsigned int ivi,ivj;
    if(df_useNbrs){
      ivi=dp_atoms[i].index+1+getAtomNeighborhood(i);
      ivj=dp_atoms[j].index+1+getAtomNeighborhood(j);
      //std::cerr<<"               "<<i<<"-"<<j<<": "<<ivi<<" "<<ivj<<std::endl;
      if(ivi<ivj)
        return -1;
      else if(ivi>ivj)
        return 1;
    }
    return 0;
  }
};


void test4(){
  BOOST_LOG(rdInfoLog) << "Testing partition refinement with neighbors." << std::endl;
  // partition refinement with neighbors
  {
    std::string smi="FC1C(Cl)CCC1C";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);
    std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
    initCanonAtoms(*m,atoms,true);
    atomcomparefunctor3 ftor(&atoms.front(),*m);
    RDKit::Canon::canon_atom *data=&atoms.front();
    int *count=(int *)malloc(atoms.size()*sizeof(int));
    int *order=(int *)malloc(atoms.size()*sizeof(int));
    int activeset;
    int *next=(int *)malloc(atoms.size()*sizeof(int));
    int *changed=(int *)malloc(atoms.size()*sizeof(int));
    memset(changed, 1, atoms.size()*sizeof(int));
    char *touched=(char *)malloc(atoms.size()*sizeof(char));

    RDKit::Canon::CreateSinglePartition(atoms.size(),order,count,data);
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);
    // std::cerr<<"1----------------------------------"<<std::endl;
    //  for(unsigned int i=0;i<m->getNumAtoms();++i){
    //    std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<" next: "<<next[order[i]]<<" changed: "<<changed[order[i]]<<std::endl;
    // }
    RDKit::Canon::RefinePartitions(*m,data,ftor,false,order,count,activeset,next,changed,touched);

    // std::cerr<<"2----------------------------------"<<std::endl;
    //  for(unsigned int i=0;i<m->getNumAtoms();++i){
    //    std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<" next: "<<next[order[i]]<<" changed: "<<changed[order[i]]<<std::endl;
    // }

    //std::cerr<<"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"<<std::endl;
    ftor.df_useNbrs=true;
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);
    // std::cerr<<"3----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //    std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<" next: "<<next[order[i]]<<" changed: "<<changed[order[i]]<<std::endl;
    // }
    RDKit::Canon::RefinePartitions(*m,data,ftor,true,order,count,activeset,next,changed,touched);

    //std::cerr<<"----------------------------------"<<std::endl;
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      //std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
      TEST_ASSERT(count[order[i]]==1);
      if(i>0){
        TEST_ASSERT(ftor(order[i],order[i-1])>=0);
      }
    }
    delete m;
  }

  {
    std::string smi="FC1C(CO)CCC1CC";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);
    std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
    initCanonAtoms(*m,atoms,true);
    atomcomparefunctor3 ftor(&atoms.front(),*m);

    RDKit::Canon::canon_atom *data=&atoms.front();
    int *count=(int *)malloc(atoms.size()*sizeof(int));
    int *order=(int *)malloc(atoms.size()*sizeof(int));
    int activeset;
    int *next=(int *)malloc(atoms.size()*sizeof(int));
    int *changed=(int *)malloc(atoms.size()*sizeof(int));
    memset(changed, 1, atoms.size()*sizeof(int));
    char *touched=(char *)malloc(atoms.size()*sizeof(char));

    RDKit::Canon::CreateSinglePartition(atoms.size(),order,count,data);
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);

    RDKit::Canon::RefinePartitions(*m,data,ftor,false,order,count,activeset,next,changed,touched);
    // std::cerr<<"----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //   std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
    // }

    ftor.df_useNbrs=true;
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);
    RDKit::Canon::RefinePartitions(*m,data,ftor,true,order,count,activeset,next,changed,touched);
    
    //std::cerr<<"----------------------------------"<<std::endl;
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      //std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
      TEST_ASSERT(count[order[i]]==1);
      if(i>0){
        //std::cerr<<"  ftor: "<<ftor(order[i],order[i-1])<<std::endl;
        TEST_ASSERT(ftor(order[i],order[i-1])>=0);
      }
    }
    delete m;
  }

  {
    std::string smi="FC1C(CC)CCC1CC";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);
    std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
    initCanonAtoms(*m,atoms,true);
    atomcomparefunctor3 ftor(&atoms.front(),*m);

    RDKit::Canon::canon_atom *data=&atoms.front();
    int *count=(int *)malloc(atoms.size()*sizeof(int));
    int *order=(int *)malloc(atoms.size()*sizeof(int));
    int activeset;
    int *next=(int *)malloc(atoms.size()*sizeof(int));
    int *changed=(int *)malloc(atoms.size()*sizeof(int));
    memset(changed, 1, atoms.size()*sizeof(int));
    char *touched=(char *)malloc(atoms.size()*sizeof(char));

    RDKit::Canon::CreateSinglePartition(atoms.size(),order,count,data);
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);

    // std::cerr<<"----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //   std::cerr<<order[i]<<" "<<atoms[order[i]].invar<<" index: "<<atoms[order[i]].index<<std::endl;
    // }

    RDKit::Canon::RefinePartitions(*m,data,ftor,false,order,count,activeset,next,changed,touched);

    //std::cerr<<"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"<<std::endl;
    ftor.df_useNbrs=true;

    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);
    RDKit::Canon::RefinePartitions(*m,data,ftor,true,order,count,activeset,next,changed,touched);
    //std::cerr<<"----------------------------------"<<std::endl;


    for(unsigned int i=0;i<m->getNumAtoms();++i){
      //std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
      if(i>0){
        //std::cerr<<"  ftor: "<<ftor(order[i],order[i-1])<<std::endl;
        TEST_ASSERT(ftor(order[i],order[i-1])>=0);
      }
    }
    
    // here we can't manage to get everything  unique
    TEST_ASSERT(order[0]==4 && count[4]==2); 
    TEST_ASSERT(order[1]==9 && count[9]==0); 
    TEST_ASSERT(order[2]==0 && count[0]==1); 
    TEST_ASSERT(order[3]==3 && count[3]==2); 
    TEST_ASSERT(order[4]==8 && count[8]==0); 
    TEST_ASSERT(order[5]==5 && count[5]==2); 
    TEST_ASSERT(order[6]==6 && count[6]==0); 
    TEST_ASSERT(order[7]==2 && count[2]==2); 
    TEST_ASSERT(order[8]==7 && count[7]==0); 
    TEST_ASSERT(order[9]==1 && count[1]==1); 

    delete m;
  }

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


void test5(){
  BOOST_LOG(rdInfoLog) << "testing canonicalization via tie breaking." << std::endl;
  // canonicalization via tie breaking
  {
    std::string smi="FC1C(CC)CCC1CC";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);
    std::vector<Canon::canon_atom> atoms(m->getNumAtoms());
    initCanonAtoms(*m,atoms,true);
    atomcomparefunctor3 ftor(&atoms.front(),*m);

    RDKit::Canon::canon_atom *data=&atoms.front();
    int *count=(int *)malloc(atoms.size()*sizeof(int));
    int *order=(int *)malloc(atoms.size()*sizeof(int));
    int activeset;
    int *next=(int *)malloc(atoms.size()*sizeof(int));
    int *changed=(int *)malloc(atoms.size()*sizeof(int));
    memset(changed, 1, atoms.size()*sizeof(int));
    char *touched=(char *)malloc(atoms.size()*sizeof(char));

    RDKit::Canon::CreateSinglePartition(atoms.size(),order,count,data);
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);

    // std::cerr<<"----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //   std::cerr<<order[i]<<" "<<atoms[order[i]].invar<<" index: "<<atoms[order[i]].index<<std::endl;
    // }

    RDKit::Canon::RefinePartitions(*m,data,ftor,false,order,count,activeset,next,changed,touched);

    //std::cerr<<"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"<<std::endl;
    ftor.df_useNbrs=true;
    RDKit::Canon::ActivatePartitions(atoms.size(),order,count,activeset,next,changed);
    RDKit::Canon::RefinePartitions(*m,data,ftor,true,order,count,activeset,next,changed,touched);

    // std::cerr<<"----------------------------------"<<std::endl;
    // for(unsigned int i=0;i<m->getNumAtoms();++i){
    //   std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
    // }

    // here we can't manage to get everything  unique
    TEST_ASSERT(order[0]==4 && count[4]==2); 
    TEST_ASSERT(order[1]==9 && count[9]==0); 
    TEST_ASSERT(order[2]==0 && count[0]==1); 
    TEST_ASSERT(order[3]==3 && count[3]==2); 
    TEST_ASSERT(order[4]==8 && count[8]==0); 
    TEST_ASSERT(order[5]==5 && count[5]==2); 
    TEST_ASSERT(order[6]==6 && count[6]==0); 
    TEST_ASSERT(order[7]==2 && count[2]==2); 
    TEST_ASSERT(order[8]==7 && count[7]==0); 
    TEST_ASSERT(order[9]==1 && count[1]==1); 

    RDKit::Canon::BreakTies(*m,data,ftor,true,order,count,activeset,next,changed,touched);
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      //std::cerr<<order[i]<<" "<<" index: "<<atoms[order[i]].index<<" count: "<<count[order[i]]<<std::endl;
      TEST_ASSERT(count[order[i]]==1);
    }
    delete m;
  }
  BOOST_LOG(rdInfoLog) << "Done" << std::endl;
};


void test6(){
  BOOST_LOG(rdInfoLog) << "testing canonicalization using the wrapper." << std::endl;
  // canonicalization using the wrapper
#if 1
  {
    std::string smi="FC1C(CC)CCC1CC";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);

    std::vector<unsigned int> atomRanks;
    RDKit::Canon::rankMolAtoms(*m,atomRanks);
    boost::dynamic_bitset<> seen(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      TEST_ASSERT(!seen[atomRanks[i]]);
      seen.set(atomRanks[i],1);
    }
    // std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    // std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[0]==2);
    TEST_ASSERT(atomRanks[1]==9);
    TEST_ASSERT(atomRanks[2]==7);
    TEST_ASSERT(atomRanks[3]==3);
    TEST_ASSERT(atomRanks[4]==0);
    TEST_ASSERT(atomRanks[5]==5);
    TEST_ASSERT(atomRanks[6]==6);
    TEST_ASSERT(atomRanks[7]==8);
    TEST_ASSERT(atomRanks[8]==4);
    TEST_ASSERT(atomRanks[9]==1);
    delete m;
  }

  {
    std::string smi="CC[C@@H]1CCC[C@@H](O1)C(=O)O";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);

    std::vector<unsigned int> atomRanks;
    RDKit::Canon::rankMolAtoms(*m,atomRanks);
    boost::dynamic_bitset<> seen(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      // std::cerr<<i<<" "<<atomRanks[i]<<std::endl;
      TEST_ASSERT(!seen[atomRanks[i]]);
      seen.set(atomRanks[i],1);
    }

    // for(unsigned int ii=0;ii<atomRanks.size();++ii){
    //    std::cerr<<ii<<":"<<atomRanks[ii]<<std::endl;
    // }
    TEST_ASSERT(atomRanks[0]==0);
    TEST_ASSERT(atomRanks[1]==4);
    TEST_ASSERT(atomRanks[2]==9);
    TEST_ASSERT(atomRanks[3]==5);
    TEST_ASSERT(atomRanks[4]==3);
    TEST_ASSERT(atomRanks[5]==6);
    TEST_ASSERT(atomRanks[6]==10);
    TEST_ASSERT(atomRanks[7]==7);
    TEST_ASSERT(atomRanks[8]==8);
    TEST_ASSERT(atomRanks[9]==1);
    TEST_ASSERT(atomRanks[10]==2);

    delete m;
  }

  {
    std::string smi="N[C@@H](Cc1c[nH]c2ccccc12)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@@H](Cc3c[nH]c4ccccc34)C(=O)OCc5ccccc5";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);

    std::vector<unsigned int> atomRanks;
    RDKit::Canon::rankMolAtoms(*m,atomRanks);
    boost::dynamic_bitset<> seen(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      // std::cerr<<i<<" "<<atomRanks[i]<<std::endl;
      TEST_ASSERT(!seen[atomRanks[i]]);
      seen.set(atomRanks[i],1);
    }

    // for(unsigned int ii=0;ii<atomRanks.size();++ii){
    //   std::cerr<<ii<<":"<<atomRanks[ii]<<std::endl;
    // }
    delete m;
  }
#endif
  {
    std::string smi="BrC=C1CCC(C(=O)O1)c2cccc3ccccc23";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);

    std::vector<unsigned int> atomRanks;
    RDKit::Canon::rankMolAtoms(*m,atomRanks);
    boost::dynamic_bitset<> seen(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      //std::cerr<<i<<" "<<atomRanks[i]<<std::endl;
      TEST_ASSERT(!seen[atomRanks[i]]);
      seen.set(atomRanks[i],1);
    }

    // for(unsigned int ii=0;ii<atomRanks.size();++ii){
    //   std::cerr<<ii<<":"<<atomRanks[ii]<<std::endl;
    // }
    delete m;
  }

  {
    std::string smi="CC12CCCC1CCCC2";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);

    // start w/o tie breaking here; we shouldn't need it.
    std::vector<unsigned int> atomRanks;
    RDKit::Canon::rankMolAtoms(*m,atomRanks,false);
    boost::dynamic_bitset<> seen(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      //      std::cerr<<"      "<<i<<" "<<atomRanks[i]<<std::endl;
      TEST_ASSERT(!seen[atomRanks[i]]);
      seen.set(atomRanks[i],1);
    }
    delete m;
  }

  {
    std::string smi="CC12CCCC1C1CCC3CC(O)CCC3(C)C1CC2";
    RWMol *m =SmilesToMol(smi);
    TEST_ASSERT(m);

    // start w/o tie breaking here; we shouldn't need it.
    std::vector<unsigned int> atomRanks;
    RDKit::Canon::rankMolAtoms(*m,atomRanks,false);
    boost::dynamic_bitset<> seen(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i){
      TEST_ASSERT(!seen[atomRanks[i]]);
      seen.set(atomRanks[i],1);
    }
    delete m;
  }


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


namespace{

  ROMol* _renumber(const ROMol *m,std::vector<unsigned int>& nVect,std::string inSmiles){
    ROMol *nm=MolOps::renumberAtoms(*m,nVect);
    TEST_ASSERT(nm);
    TEST_ASSERT(nm->getNumAtoms()==m->getNumAtoms());
    TEST_ASSERT(nm->getNumBonds()==m->getNumBonds());
    MolOps::assignStereochemistry(*nm,true,true);
    for(unsigned int ii=0;ii<nm->getNumAtoms();++ii){
      if(nm->getAtomWithIdx(ii)->hasProp("_CIPCode")){
        TEST_ASSERT(m->getAtomWithIdx(nVect[ii])->hasProp("_CIPCode"));
        std::string ocip=m->getAtomWithIdx(nVect[ii])->getProp<std::string>("_CIPCode");
        std::string ncip=nm->getAtomWithIdx(ii)->getProp<std::string>("_CIPCode");
        if(ocip!=ncip){
          std::cerr<<"  cip mismatch: "<<inSmiles<<std::endl;
          std::cerr<<"      "<<nVect[ii]<<": "<<ocip<<" -> "<<ii<<": "<<ncip<<std::endl;
          std::cerr<<"      "<<MolToSmiles(*nm,true)<<std::endl;
        }
        TEST_ASSERT(ocip==ncip);
      }
    }
    return nm;
  }

  void _renumberTest(const ROMol *m,std::string inSmiles,unsigned int numRenumbers){
    PRECONDITION(m,"no molecule");
//    std::cerr<<">>>>>>>>>>>>>>>>>>>>>>>>>>>"<<std::endl;
    std::string osmi=MolToSmiles(*m,true);
    std::vector<unsigned int> idxV(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i) idxV[i]=i;

    std::srand(0xF00D);
    for(unsigned int i=0;i<numRenumbers;++i){
//      std::cerr<<"---------------------------------------------------"<<std::endl;
      std::vector<unsigned int> nVect(idxV);
      std::random_shuffle(nVect.begin(),nVect.end());
//      for(unsigned int j=0;j<m->getNumAtoms();++j){
//        std::cerr<<"Renumber: "<<nVect[j]<<"->"<<j<<std::endl;
//      }
      ROMol *nm= _renumber(m,nVect,inSmiles);
      
      std::string smi=MolToSmiles(*nm,true);
      if(smi!=osmi){
        std::cerr<<"  input: "<<inSmiles<<", Renumbering round: " << i <<std::endl;
        std::cerr<<osmi<<std::endl;
        std::cerr<<smi<<std::endl;
        m->setProp("_Name","orig");
        std::cerr<<MolToMolBlock(*m)<<std::endl;
        nm->setProp("_Name","renumber");
        std::cerr<<MolToMolBlock(*nm)<<std::endl;
        for(unsigned int j=0;j<m->getNumAtoms();++j){
          std::cerr<<"Renumber: "<<nVect[j]<<"->"<<j<<std::endl;
        }
      }
      TEST_ASSERT(smi==osmi);
      delete nm;
    }
  }

  void _renumberTest2(const ROMol *m,std::string inSmiles,unsigned int numRenumbers){
    PRECONDITION(m,"no molecule");

    unsigned int nAtoms=m->getNumAtoms();
    std::vector<unsigned int> idxV(m->getNumAtoms());
    for(unsigned int i=0;i<m->getNumAtoms();++i) idxV[i]=i;

    std::srand(0xF00D);
    for(unsigned int i=0;i<numRenumbers;++i){
      std::vector<unsigned int> nVect(idxV);
      std::random_shuffle(nVect.begin(),nVect.end());

      ROMol *nm= _renumber(m,nVect,inSmiles);

      UINT_VECT ranks(nAtoms);
      Canon::rankMolAtoms(*nm,ranks,true);
      char *ranksSet=(char *)malloc(nAtoms*sizeof(char));
      memset(ranksSet,0,nAtoms*sizeof(char));
      for(unsigned int i=0;i<ranks.size();i++){
        ranksSet[ranks[i]]=1;
      }
      for(unsigned int i=0;i<nAtoms;i++){
        if(ranksSet[i]!=1){
          std::cerr << "Molecule has non unique ranks: " << MolToSmiles(*nm,true) <<  ", Renumbering round: " << i <<std::endl;
          for(unsigned int i=0;i<nAtoms;i++){
            std::cerr << "AtomIdx: " << i << " Rank: " << ranks[i] << std::endl;
          }
        }
        TEST_ASSERT(ranksSet[i]==1);
      }
      delete nm;
    }
  }
}

void test7a() {
  BOOST_LOG(rdInfoLog) << "testing some specific ordering problems" << std::endl;
  std::string rdbase = getenv("RDBASE");
  std::string smi1,smi2;
  {
    std::string fName = rdbase+"/Code/GraphMol/test_data/canon_reorder1.mol";
    RWMol *m = MolFileToMol(fName,false,false);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
//    std::cerr <<"\n\n\n\n\n\n\n\n\n\n\n\n>--------------" << std::endl;
    RDKit::Canon::rankMolAtoms(*m,atomRanks,false);
//    std::cerr <<"---------------" << std::endl;
//    for(unsigned int i=0;i<m->getNumAtoms();++i){
//      std::cerr<<" "<<i+1<<" "<<atomRanks[i]<<std::endl;
//    }
//    std::cerr <<"---------------" << std::endl;
    smi1=MolToSmiles(*m,true);
    delete m;
  }
  {
    std::string fName = rdbase+"/Code/GraphMol/test_data/canon_reorder2.mol";
    RWMol *m = MolFileToMol(fName,false,false);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
//    std::cerr <<">--------------" << std::endl;
    RDKit::Canon::rankMolAtoms(*m,atomRanks,false);
//    std::cerr <<"---------------" << std::endl;
//    for(unsigned int i=0;i<m->getNumAtoms();++i){
//      std::cerr<<" "<<i+1<<" "<<atomRanks[i]<<std::endl;
//    }
//    std::cerr <<"---------------" << std::endl;
    smi2=MolToSmiles(*m,true);
    delete m;
  }
  if(smi1!=smi2){
    std::cerr<<smi1<<"\n"<<smi2<<std::endl;
  }
  TEST_ASSERT(smi1==smi2);
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

std::string smis[]={
  "C[C@@H]1CCC[C@H](C)[C@H]1C",
  "N[C@@]1(C[C@H]([18F])C1)C(=O)O",
  "CC12CCCC1C1CCC3CC(O)CCC3(C)C1CC2",
  "CC(C)CCCC[C@@H]1C[C@H](/C=C/[C@]2(C)CC[C@H](O)CC2)[C@@H](O)[C@H]1O",
  "C[C@@]12CCC[C@H]1[C@@H]1CC[C@H]3C[C@@H](O)CC[C@]3(C)[C@H]1CC2",
  "CCCN[C@H]1CC[C@H](NC)CC1",
  "O=S(=O)(NC[C@H]1CC[C@H](CNCc2ccc3ccccc3c2)CC1)c1ccc2ccccc2c1",
  "CC(C)[C@H]1CC[C@H](C(=O)N[C@H](Cc2ccccc2)C(=O)O)CC1",
  "O=[N+]([O-])c1ccccc1S(=O)(=O)NC[C@H]1CC[C@H](CNCC2Cc3ccccc3CC2)CC1",
  "Oc1ccc2c(Cc3ccc(OCCN4CCCCC4)cc3)c([C@H]3CC[C@H](O)CC3)sc2c1",
  "O=C(c1ccc(OCCN2CCCCC2)cc1)c1c2ccc(O)cc2sc1[C@H]1CC[C@H](O)CC1",
  "N#Cc1ccc2c(c1)CCN(CC[C@@H]1CC[C@@H](NC(=O)c3ccnc4ccccc34)CC1)C2",
  "COCCOC[C@H](CC1(C(=O)N[C@H]2CC[C@@H](C(=O)O)CC2)CCCC1)C(=O)O",
  "c1ccc(CN[C@H]2CC[C@H](Nc3ccc4[nH]ncc4c3)CC2)cc1",
  "CCC1=C(C)CN(C(=O)NCCc2ccc(S(=O)(=O)NC(=O)N[C@H]3CC[C@H](C)CC3)cc2)C1=O",
  "C[C@H]1C[C@H](C1)N1CCC1",
  "C[C@H]1C[C@H](C1)N1CCN(C)CC1",
  "CN1CCN(CC1)[C@H]1C[C@H](C1)c1ncc2c(N)nccn12",
  "CN1CCN(CC1)[C@H]1C[C@H](C1)c1nc(-c2ccc3ccc(nc3c2)-c2ccccc2)c2c(N)nccn12",
  "C12C3C1C3C4C5C4C52",
  "N[C@H]1C2CC3CC1C[C@](O)(C3)C2",
  "O=C(CN1CCN(c2ccc(C(F)(F)F)cn2)CC1)N[C@H]1C2CC3CC1C[C@](O)(C3)C2",
  "COc1cc([C@H]2[C@H](C)[C@H](C)[C@H]2c2ccc(O)c(OC)c2)ccc1O",
  "N[C@@H]1[C@H]2CNC[C@@H]12",
  "N[C@@H]1[C@H]2CN(c3nc4c(cc3F)c(=O)c(C(=O)O)cn4C3CC3)C[C@@H]12",
  // some examples that came up while doing a torture test in ZINC
  "CN1CCCNCCN(C)CCC[NH2+]CC1",
  "CN1CCC[NH2+]CCN(C)CCC[NH+](C)CC1",
  "O=P([O-])([O-])C[NH+]1CCCN(CP(=O)([O-])O)CC[NH+](CP(=O)([O-])[O-])CCC[NH+](CP(=O)([O-])[O-])CC1",
  "O=C(CCNC(=O)Cn1cnc2ccccc2c1=O)NCCc1c[nH]c2ccccc12",
  "C1CNCC[NH2+]CC(C2CNCC[NH2+]CCC[NH2+]CCNC2)CNCC[NH2+]C1",
  // C60
  "C12=C3C4=C5C6=C1C7=C8C9=C1C%10=C%11C(=C29)C3=C2C3=C4C4=C5C5=C9C6=C7C6=C7C8=C1C1=C8C%10=C%10C%11=C2C2=C3C3=C4C4=C5C5=C%11C%12=C(C6=C95)C7=C1C1=C%12C5=C%11C4=C3C3=C5C(=C81)C%10=C23",
  // C70
  "C12=C3C4=C5C6=C7C8=C9C%10=C%11C%12=C%13C%10=C%10C8=C5C1=C%10C1=C%13C5=C8C1=C2C1=C3C2=C3C%10=C%13C%14=C3C1=C8C1=C3C5=C%12C5=C8C%11=C%11C9=C7C7=C9C6=C4C2=C2C%10=C4C(=C29)C2=C6C(=C8C8=C9C6=C4C%13=C9C(=C%141)C3=C85)C%11=C27",
  //Bernd's example1
  "C12C3C4C3C3C1C2C43",
  //Bernd's example2
  "C12C3C1C1C4C5C4C4C6C(C6C3C3C1C43)C25",
  //doubled house
  "C12C3C45C67C8C9C66C14C21C35C78C961",
  "C12C3C45C6C7C11C27C41C356",
  //Problematic round-tripping
  "COC(=O)/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(/C)/C=C/C=C(\\C)/C=C/C(=O)[O-]",
  "COC(=O)/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(\\C)/C=C/C=C(\\C)/C=C/C(=O)[O-]",
  "c1cc2ccc(ccc3ccc1cc3)cc2",
  "C13C6C1C2C4C2C3C5C4C56",
  "C45C1C6C3C6C5C4C2C3C12",
  "C45C2C6C3C6C5C4C1C3C12",
  "Cl[C@H]1[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H]1Cl",
  "N[C@]1(C(=O)O)C[C@H](n2oc(=O)[nH]c2=O)C1",
  "CC1CC(C)CC(C)C1",
  "C[C@H]1C[C@@H](C)C[C@H](C)C1",
  "C[C@H]1C[C@@H](C)C[C@@H](C)C1",
  //Stereochemistry in large rings
  "C1[C@@H](C(C)=O)[C@H]2[C@H](C(C)=C1)[C@@H]1O[C@H]2[C@@H](O)C/C=C\\CC1",
  //Chembl 20 examples
  "COC(=O)CC[C@]12C[C@]13CC[C@]1(C)[C@@H]4[C@@H](C[C@@]1(C)[C@@H]3CC[C@H]2C(C)(C)O)O[C@@]1(C[C@@H](C)C(=O)O1)C[C@H]4C",
  "C/C=C/[C@H](O)C(C)(C)[C@@H]1CC=CC=CC=C[C@H](OC)Cc2nc(co2)C(=O)O[C@H](C(C)(C)[C@@H](O)/C=C/C)CC=C[C@H]2O[C@H]2C=CC=Cc2nc(co2)C(=O)O1",
  "N[C@]1(C(=O)O)C[C@@H](n2oc(=O)[nH]c2=O)C1",
  "COc1ccc([C@H]2C3(CO)C4[N@](C)C5C2(CO)C2[N@](C)C3C4(CO)[C@H](c3ccc(OC)cc3)C52CO)cc1",
  "NCCNC(=O)[C@]1(O)C[C@@H](O)[C@H](O)[C@H](O)C1",
  //CIP renumber problems
//  "O=P(O)(O)O[C@@H]1[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O)[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O[32P](=O)(O)O)[C@@H]1OP(=O)(O)O",
//  "O=C(NCCO[C@H]1[C@@H](O)[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O)[C@H](O)[C@H]1OP(=O)(O)O)NCCO[C@H]1[C@@H](O)[C@H](OP(=O)(O)O)[C@@H](O[PH](O)(O)O)[C@H](O)[C@H]1OP(=O)(O)O",
//  "O=C(NCCO[C@@H]1[C@H](OP(=O)(O)O)[C@@H](OP(=O)(O)O)[C@H](O[PH](O)(O)O)[C@@H](OP(=O)(O)O)[C@@H]1OP(=O)(O)O)NCCO[C@H]1[C@@H](OP(=O)(O)O)[C@H](O)[C@@H](OP(=O)(O)O)[C@H](OP(=O)(O)O)[C@H]1O",
//  "O=C(O)[C@H]1[C@@H](C(=O)O)[C@@H](C(=O)O)[C@@H]1C(=O)O",
  "C[C@H]1[C@H](C)[C@@H](C)[C@H]1C",
  "COc1cc([C@H]2[C@@](NC(=O)c3ccc(NC(=O)C4CCCC4)cc3)(C(=O)O)[C@@H](c3ccc(OC(=O)c4cccs4)c(OC)c3)[C@]2(NC(=O)c2ccc(NC(=O)C3CCCC3)cc2)C(=O)O)ccc1OC(=O)c1cccs1",
  "COc1cc([C@H]2[C@@](NC(=O)c3ccc(NC(=O)OC(C)(C)C)cc3)(C(=O)O)[C@@H](c3ccc(OC(=O)c4cccs4)c(OC)c3)[C@]2(NC(=O)c2ccc(NC(=O)OC(C)(C)C)cc2)C(=O)O)ccc1OC(=O)c1cccs1",
  "COc1cc([C@H]2[C@](NC(=O)c3ccc(NC(=O)OC(C)(C)C)cc3)(C(=O)O)[C@H](c3ccc(OC(=O)c4cccs4)c(OC)c3)[C@]2(NC(=O)c2ccc(NC(=O)OC(C)(C)C)cc2)C(=O)O)ccc1OC(=O)c1cccs1",
  "CCC[C@H]1CC[C@H]([C@H]2CC[C@H](OC(=O)[C@H]3[C@@H](c4ccc(O)cc4)[C@H](C(=O)O[C@H]4CC[C@H]([C@H]5CC[C@H](CCC)CC5)CC4)[C@@H]3c3ccc(O)cc3)CC2)CC1",
    //test molecules with atom-mapping numbers
  "[O:1]=[C:2]([CH2:3][C:4]1=[CH:5][CH:6]=[CH:7][CH:8]=[CH:9]1)[NH2:10]",
  //chembl molecules with multiple fragments
  //CHEMBL439119
  "CCCCCCC1C23C4=c5c6c7c8c9c%10c%11c%12c%13c%14c%15c%16c%17c%18c%19c%20c%21c%22c%23c(c5c5c6c6c8c%11c8c%11c%12c%15c%12c(c%20%16)c%21c%15c%23c5c(c68)c%15c%12%11)C2(C[N+]1(C)C)C%22C%19c1c-%18c2c5c(c13)C4C7C9=C5C1(C2C%17%14)C(CCCCCC)[N+](C)(C)CC%10%131.[I-].[I-]",
  //CHEMBL1203199
  "C[C@H](NC(=O)[C@H]1Cc2c(sc3ccccc23)CN1)c1ccccc1.Cl",
  //CHEMBL501667
  "CCn1c2ccc3cc2c2cc(ccc21)C(=O)c1ccc(cc1)Cn1cc[n+](c1)Cc1ccc(cc1)-c1cccc(-c2ccc(cc2)C[n+]2ccn(c2)Cc2ccc(cc2)C3=O)c1C(=O)O.[Br-].[Br-]",
  //CHEMBL12438
  "CCCCCCCCCCCCCCCCCCNC(=O)OC[C@H]1C[C@H]([C@@H2]OC(=O)N(Cc2cccc[n+]2CC)C(C)=O)C1.[I-]",
  //CHEMBL1172371
  "CC.CCCCCCCCCC(C(=O)NCCc1ccc(OP(=S)(Oc2ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc2)N(C)/N=C/c2ccc(OP3(Oc4ccc(/C=N/N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)cc4)=NP(Oc4ccc(/C=N/N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)cc4)(Oc4ccc(/C=N/N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)cc4)=NP(Oc4ccc(/C=N/N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)cc4)(Oc4ccc(/C=N/N(C)P(=S)(Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)Oc5ccc(CCNC(=O)C(CCCCCCCCC)P(=O)([O-])O)cc5)cc4)=N3)cc2)cc1)P(=O)([O-])O.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO.CCCCCCCCCCCCCCCC[NH2+]OC(CO)C(O)C(OC1OC(CO)C(O)C(O)C1O)C(O)CO",
   //Examples first reviewer
  "C12C3C4C1C3C1C3C4C1C23", // does not initially work
  "C12C3C1C1C4C5C(C23)C5C14",
  "C12C3C4C5C1C1C4C5C3C21",
  "C12C3C4C1C2C1C2C4C2C31",
  "C12C3C4C5C2C2C6C1C(C5C36)C42",
  "C12C3C4C5C1C1C3C3C5C1C2C43",
  "C12C3C4C5C6C1C1C7C3C3C5C1C1C6C3C2C7C41", // does not initially work
  "C12C3C4C5C6C1C1C7C3C3C6C6C4C7C2C3C5C16",
  "C12C3C4C5C6C7C8C9C1C6C1C(C37)C9C5C2C8C41",
  "C12C3C4C5C6C7C1C1C8C4C4C9C2C2C5C5C1C1C3C(C7C45)C2C8C6C91", // does not initially work
  "C12C3C4C5C6C7C1C1C8C4C4C7C7C3C3C8C8C2C2C5C3C4C(C1C72)C68",
  "C12C3C4C5C6C7C8C1C1C9C5C5C%10C2C2C%11C%12C%13C3C3C7C%10C7C4C%11C1C3C(C5C8%12)C(C62)C7C9%13", // does not initially work
  //drawn examples first reviewer
  "C12C3C4C1CC5C46C7C5C1C57C6C53C1C2",
  "C1C2C3C4CC5C6C1C17C8C61C5C48C3C27",
  "EOS"
};

void test7(){
  BOOST_LOG(rdInfoLog) << "testing stability w.r.t. renumbering." << std::endl;
  unsigned int i=0;
  while(smis[i]!="EOS"){
    std::string smiles=smis[i++];
    ROMol *m = SmilesToMol(smiles);
    TEST_ASSERT(m);
    MolOps::assignStereochemistry(*m,true);
    _renumberTest(m,smiles,500);
    delete m;
  }
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

std::string molbl1 =
"CHEMBL1950780                                                        \n"
"     RDKit          2D                                               \n"
"                                                                     \n"
" 12 12  0  0  0  0  0  0  0  0999 V2000                              \n"
"   16.2083   -6.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   16.2083   -7.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   16.9204   -7.4083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   17.6324   -7.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   17.6324   -6.1750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   16.9204   -5.7583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   16.9204   -4.9333    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   18.3480   -5.7646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   18.3462   -7.4135    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   16.9204   -8.2333    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   15.4945   -7.4135    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   15.4927   -5.7646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n"
"  5  6  1  0                                                         \n"
"  6  7  1  6                                                         \n"
"  1  2  1  0                                                         \n"
"  5  8  1  6                                                         \n"
"  1  6  1  0                                                         \n"
"  4  9  1  6                                                         \n"
"  2  3  1  0                                                         \n"
"  3 10  1  1                                                         \n"
"  3  4  1  0                                                         \n"
"  2 11  1  6                                                         \n"
"  4  5  1  0                                                         \n"
"  1 12  1  6                                                         \n"
"M  END";

std::string molbl2 =
"CHEMBL1874247                                                        \n"
"     RDKit          2D                                               \n"
"                                                                     \n"
" 12 12  0  0  0  0  0  0  0  0999 V2000                              \n"
"    0.0000    1.6500    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n"
"    1.4289    0.8250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n"
"   -1.4289    0.8250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n"
"    1.4289   -0.8250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n"
"   -1.4289   -0.8250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n"
"    0.0000   -1.6500    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0\n"
"    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
"  7  1  1  1                                                         \n"
"  8  2  1  1                                                         \n"
"  9  3  1  1                                                         \n"
" 10  4  1  6                                                         \n"
" 11  5  1  6                                                         \n"
" 12  6  1  1                                                         \n"
"  7  8  1  0                                                         \n"
"  7  9  1  0                                                         \n"
"  8 10  1  0                                                         \n"
"  9 11  1  0                                                         \n"
" 10 12  1  0                                                         \n"
" 11 12  1  0                                                         \n"
"M  END";


void test8(){
  BOOST_LOG(rdInfoLog) << "testing smiles round-tripping." << std::endl;
  std::string rdbase = getenv("RDBASE");
  {
    std::string fName = rdbase+"/Code/GraphMol/test_data/iChi1b.mol";
    RWMol *m = MolFileToMol(fName);
    TEST_ASSERT(m);
    std::string smi1=MolToSmiles(*m,true);
    delete m;
    m = SmilesToMol(smi1);
    TEST_ASSERT(m);
    std::string smi2=MolToSmiles(*m,true);
    if(smi1!=smi2) std::cerr<<smi1<<"\n"<<smi2<<std::endl;
    TEST_ASSERT(smi1==smi2);
    delete m;
  }

  {
    unsigned int i=0;
    while(smis[i]!="EOS"){
      std::string smiles=smis[i++];
      ROMol *m = SmilesToMol(smiles);
      TEST_ASSERT(m);
//      std::cerr<<"MolToSMILES 1"<<std::endl;
      std::string smi1=MolToSmiles(*m, true);
      delete m;

      m = SmilesToMol(smi1);
      TEST_ASSERT(m);
//      std::cerr<<"MolToSMILES 2"<<std::endl;
      std::string smi2=MolToSmiles(*m, true);
      delete m;
      if(smi1!=smi2){
        std::cerr<<"Input smiles: "<<smiles<<"\n1. Iter: "<<smi1<<"\n2. Iter: "<<smi2<<std::endl;
      }
      TEST_ASSERT(smi1==smi2);
    }
    {
      ROMol *m = MolBlockToMol(molbl1);
      TEST_ASSERT(m);
      std::string smiles=MolToSmiles(*m, true);
      delete m;

      m = SmilesToMol(smiles);
      TEST_ASSERT(m);
      //      std::cerr<<"MolToSMILES 1"<<std::endl;
      std::string smi1=MolToSmiles(*m, true);
      delete m;

      if(smiles!=smi1){
        std::cerr<<smiles<<"\n"<<smi1<<std::endl;
      }
      TEST_ASSERT(smiles==smi1);
    }
    {
      ROMol *m = MolBlockToMol(molbl2);
      TEST_ASSERT(m);
      std::string smiles=MolToSmiles(*m, true);
      delete m;

      m = SmilesToMol(smiles);
      TEST_ASSERT(m);
      //      std::cerr<<"MolToSMILES 1"<<std::endl;
      std::string smi1=MolToSmiles(*m, true);
      delete m;

      if(smiles!=smi1){
        std::cerr<<smiles<<"\n"<<smi1<<std::endl;
      }
      TEST_ASSERT(smiles==smi1);
    }
  }

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

void test9(){
  BOOST_LOG(rdInfoLog) << "testing chiral invariants." << std::endl;
  std::string rdbase = getenv("RDBASE");

  {
    std::string smi="C[C@](F)(Cl)I";
    RWMol *m =SmilesToMol(smi,0,0);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
    //std::cerr<<smi<<std::endl;
    RDKit::Canon::chiralRankMolAtoms(*m,atomRanks);
    //std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    //std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[0]<atomRanks[2]);
    TEST_ASSERT(atomRanks[0]<atomRanks[3]);
    TEST_ASSERT(atomRanks[0]<atomRanks[4]);
    TEST_ASSERT(atomRanks[2]<atomRanks[3]);
    TEST_ASSERT(atomRanks[2]<atomRanks[4]);
    TEST_ASSERT(atomRanks[3]<atomRanks[4]);
  }

  {
    std::string smi="CC[C@](F)(Cl)C=C";
    RWMol *m =SmilesToMol(smi,0,0);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
    //std::cerr<<smi<<std::endl;
    RDKit::Canon::chiralRankMolAtoms(*m,atomRanks);
    //std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    //std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[1]<atomRanks[3]);
    TEST_ASSERT(atomRanks[1]<atomRanks[4]);
    TEST_ASSERT(atomRanks[1]<atomRanks[5]);
    TEST_ASSERT(atomRanks[3]<atomRanks[4]);
    TEST_ASSERT(atomRanks[4]>atomRanks[5]);
    TEST_ASSERT(atomRanks[4]>atomRanks[5]);
  }

  {
    // make sure we aren't breaking ties
    std::string smi="C[C@](C)(Cl)I";
    RWMol *m =SmilesToMol(smi,0,0);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
    //std::cerr<<smi<<std::endl;
    RDKit::Canon::chiralRankMolAtoms(*m,atomRanks);
    //std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    //std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[0]==atomRanks[2]);
    TEST_ASSERT(atomRanks[0]<atomRanks[3]);
    TEST_ASSERT(atomRanks[0]<atomRanks[4]);
    TEST_ASSERT(atomRanks[2]<atomRanks[3]);
    TEST_ASSERT(atomRanks[2]<atomRanks[4]);
    TEST_ASSERT(atomRanks[3]<atomRanks[4]);
  }

  {
    std::string smi="N[C@H]1C2CC3CC1C[C@](O)(C3)C2";
    RWMol *m =SmilesToMol(smi,0,0);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
    //std::cerr<<smi<<std::endl;
    RDKit::Canon::chiralRankMolAtoms(*m,atomRanks);
    //std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    //std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[0]>atomRanks[1]);
    TEST_ASSERT(atomRanks[0]<atomRanks[9]);
    TEST_ASSERT(atomRanks[2]==atomRanks[6]);
    TEST_ASSERT(atomRanks[7]==atomRanks[11]);
    TEST_ASSERT(atomRanks[3]==atomRanks[5]);
    TEST_ASSERT(atomRanks[2]>atomRanks[3]);
    TEST_ASSERT(atomRanks[2]>atomRanks[11]);
    TEST_ASSERT(atomRanks[3]<atomRanks[11]);
  }

  {
    // this one was a chiral ranking problem 
    std::string smi="COC(C)CC(C)(C)O";
    RWMol *m =SmilesToMol(smi,0,0);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
    //std::cerr<<smi<<std::endl;
    RDKit::Canon::chiralRankMolAtoms(*m,atomRanks);
    //std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    //std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[1]>atomRanks[8]);
    TEST_ASSERT(atomRanks[5]>atomRanks[2]);
  }
  
  {
    // are double bonds being handled correctly?
    std::string smi="OC[C@H](F)C=O";
    RWMol *m =SmilesToMol(smi,0,0);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
    //std::cerr<<smi<<std::endl;
    RDKit::Canon::chiralRankMolAtoms(*m,atomRanks);
    //std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    //std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[0]<atomRanks[5]);
    TEST_ASSERT(atomRanks[1]<atomRanks[4]);
  }

  {
    // are double bonds being handled correctly?
    std::string smi="O=C[C@H](F)CO";
    RWMol *m =SmilesToMol(smi,0,0);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
    //std::cerr<<smi<<std::endl;
    RDKit::Canon::chiralRankMolAtoms(*m,atomRanks);
    //std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    //std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[0]>atomRanks[5]);
    TEST_ASSERT(atomRanks[1]>atomRanks[4]);
  }

  {
    // are double bonds being handled correctly?
    std::string smi="CC[C@](C)(CF)C=O";
    RWMol *m =SmilesToMol(smi,0,0);
    TEST_ASSERT(m);
    MolOps::sanitizeMol(*m);
    std::vector<unsigned int> atomRanks;
    //std::cerr<<smi<<std::endl;
    RDKit::Canon::chiralRankMolAtoms(*m,atomRanks);
    //std::copy(atomRanks.begin(),atomRanks.end(),std::ostream_iterator<unsigned int>(std::cerr," "));
    //std::cerr<<std::endl;
    TEST_ASSERT(atomRanks[4]>atomRanks[6]);
    TEST_ASSERT(atomRanks[1]<atomRanks[4]);
  }

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


void test10(){
  BOOST_LOG(rdInfoLog) << "testing unique ranks in w.r.t. renumbering." << std::endl;
  unsigned int i=0;
  while(smis[i]!="EOS"){
    std::string smiles=smis[i++];
//    std::cerr<< ">>>Molecule: " << smiles << std::endl;
    ROMol *m = SmilesToMol(smiles);
    TEST_ASSERT(m);
    MolOps::assignStereochemistry(*m,true);
    _renumberTest2(m,smiles,1);
    delete m;
  }
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}


void test11(){
  BOOST_LOG(rdInfoLog) << "testing mol fragments." << std::endl;
  {
    std::string smi="C[C@H]([C@H](c1ccccc1)O)N2CCCCC2.C[C@@H]([C@H](c1ccccc1)O)N2CCCCC2";
    ROMol *m = SmilesToMol(smi);
    TEST_ASSERT(m);
    std::vector<std::string> vfragsmi;
    std::vector<std::vector<int> > frags;
    unsigned int numFrag = MolOps::getMolFrags(*m,frags);
    for(unsigned i=0;i<numFrag;++i){
      std::string smii = MolFragmentToSmiles(*m,frags[i],0,0,0,true);
      //std::cout << "Test "<< smii << std::endl;
      vfragsmi.push_back(smii);
    }
    std::string smi1 = MolToSmiles(*m,true);
    delete m;

    smi="C[C@@H]([C@H](c1ccccc1)O)N2CCCCC2.C[C@H]([C@H](c1ccccc1)O)N2CCCCC2";
    m = SmilesToMol(smi);
    TEST_ASSERT(m);
    std::string smi2 = MolToSmiles(*m,true);
    delete m;
    //std::cout << smi1 << "\n" << smi2 << std::endl;
    TEST_ASSERT(smi1==smi2);

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

void test12(){
  BOOST_LOG(rdInfoLog) << "testing protein round-tripping." << std::endl;
  std::string rdbase = getenv("RDBASE");
  {
    std::string fName = rdbase+"/Code/GraphMol/FileParsers/test_data/2FVD.pdb";
    ROMol *m = PDBFileToMol(fName);
    TEST_ASSERT(m);
    std::string smi1 = MolToSmiles(*m,true);
    delete m;

    m = SmilesToMol(smi1);
    TEST_ASSERT(m);
    std::string smi2 = MolToSmiles(*m,true);
    delete m;
    //std::cout << smi1 << "\n" << smi2 << std::endl;
    TEST_ASSERT(smi1==smi2);
  }
  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}

int main(){
  RDLog::InitLogs();
#if 1
  test1();
  test2();
  test3();
  test4();
  test5();
  test6();
  test7a();
  test9();
  test10();
  test11();
  test12();
  test7();
  test8();
#endif

  return 0;
}