// $Id$
//
//  Copyright (C) 2003-2010 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/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/Fingerprints/MorganFingerprints.h>
#include <GraphMol/Fingerprints/MACCS.h>
#include <GraphMol/Fingerprints/AtomPairs.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <DataStructs/ExplicitBitVect.h>
#include <DataStructs/BitOps.h>
#include <RDGeneral/RDLog.h>
#include <string>
#include <boost/version.hpp>
#include <boost/foreach.hpp>

using namespace RDKit;

void test1(){
  BOOST_LOG(rdInfoLog) <<"testing basics" << std::endl;
  {
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1->getNumAtoms()==6);
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1);
    ExplicitBitVect *fp2=RDKFingerprintMol(*m1);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>=0.0);
  
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    delete fp2;
    fp2=RDKFingerprintMol(*m2);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);

    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }

  {
    std::string smi = "Cc1ccc(C(F)(F)F)o1";
    RWMol *m1 = SmilesToMol(smi);
    std::vector<boost::uint32_t> vs1(m1->getNumAtoms());
    for(unsigned int i=0;i<m1->getNumAtoms();++i){
      vs1[i] = m1->getAtomWithIdx(i)->getAtomicNum();
    }
  std::cerr<<"\n\n\n\n\n\n\n\n\n-------------------"<<std::endl;
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,5,1024,1,0,-1,0,1,1,&vs1);
    smi = "c1ccoc1";
    RWMol *m2 = SmilesToMol(smi);
    std::vector<boost::uint32_t> vs2(m2->getNumAtoms());
    for(unsigned int i=0;i<m2->getNumAtoms();++i){
      vs2[i] = m2->getAtomWithIdx(i)->getAtomicNum();
    }
  std::cerr<<"\n\n\n\n\n\n\n\n\n-------------------"<<std::endl;
    ExplicitBitVect *fp2=RDKFingerprintMol(*m2,1,5,1024,1,0,-1,0,1,1,&vs2);

    TEST_ASSERT(((*fp1)&(*fp2))==(*fp2));
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }

  {
    std::string smi = "Oc1cc2[nH]cnc2c(O)n1";
    RWMol *m1 = SmilesToMol(smi);
    std::vector<boost::uint32_t> vs1(m1->getNumAtoms());
    for(unsigned int i=0;i<m1->getNumAtoms();++i){
      vs1[i] = m1->getAtomWithIdx(i)->getAtomicNum();
    }
    m1->debugMol(std::cerr);
  std::cerr<<"\n\n\n\n\n\n\n\n\n-------------------"<<std::endl;
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,4,4,1024,1,0,-1,0,1,1,&vs1);

    for(unsigned int i=0;i<m1->getNumAtoms();++i){
      smi = MolToSmiles(*m1,false,false,i,false);
      RWMol *m2 = SmilesToMol(smi);
      std::vector<boost::uint32_t> vs2(m2->getNumAtoms());
      for(unsigned int i=0;i<m2->getNumAtoms();++i){
        vs2[i] = m2->getAtomWithIdx(i)->getAtomicNum();
      }
      std::cerr<<"SMI: "<<smi<<std::endl;
      m2->debugMol(std::cerr);
      std::cerr<<"\n\n\n\n\n\n\n\n\n-------------------"<<std::endl;
      ExplicitBitVect *fp2=RDKFingerprintMol(*m2,4,4,1024,1,0,-1,0,1,1,&vs2);
      IntVect iv;
      ((*fp2)^(*fp1)).getOnBits(iv);
      std::copy(iv.begin(),iv.end(),std::ostream_iterator<int>(std::cerr,", "));
      std::cerr<<std::endl;
      
      TEST_ASSERT((*fp1)==(*fp2));
      delete m2;
      delete fp2;
    }
  }
  {
    std::string smi = "Oc1cc2[nH]cnc2c(O)n1";
    RWMol *m1 = SmilesToMol(smi);
    std::vector<boost::uint32_t> vs1(m1->getNumAtoms());
    for(unsigned int i=0;i<m1->getNumAtoms();++i){
      vs1[i] = m1->getAtomWithIdx(i)->getAtomicNum();
    }
  std::cerr<<"\n\n\n\n\n\n\n\n\n-------------------"<<std::endl;
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,5,1024,1,0,-1,0,1,1,&vs1);
    smi = "c1ccncc1";
    RWMol *m2 = SmilesToMol(smi);
    std::vector<boost::uint32_t> vs2(m2->getNumAtoms());
    for(unsigned int i=0;i<m2->getNumAtoms();++i){
      vs2[i] = m2->getAtomWithIdx(i)->getAtomicNum();
    }
  std::cerr<<"\n\n\n\n\n\n\n\n\n-------------------"<<std::endl;
    ExplicitBitVect *fp2=RDKFingerprintMol(*m2,1,5,1024,1,0,-1,0,1,1,&vs2);

    IntVect iv;
    ((*fp2)^((*fp1)&(*fp2))).getOnBits(iv);
    std::copy(iv.begin(),iv.end(),std::ostream_iterator<int>(std::cerr,", "));
    std::cerr<<std::endl;
    
    TEST_ASSERT(((*fp1)&(*fp2))==(*fp2));
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }


  
  BOOST_LOG(rdInfoLog) <<"done" << std::endl;
}
void test2(){
  BOOST_LOG(rdInfoLog) <<"testing subgraph invariants" << std::endl;

  std::string smi = "CC(=O)COC";
  RWMol *m1 = SmilesToMol(smi);
  TEST_ASSERT(m1->getNumAtoms()==6);
  BOOST_LOG(rdInfoLog) <<"--------------------  fp1 " << std::endl;
  ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,4,2048,4,false);
  BOOST_LOG(rdInfoLog) <<"--------------------  fp2 " << std::endl;
  ExplicitBitVect *fp2=RDKFingerprintMol(*m1,1,4,2048,4,false);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);
  
  RWMol *m2 = SmilesToMol("CC");
  delete fp2;
  BOOST_LOG(rdInfoLog) <<"--------------------  fp2 " << std::endl;
  fp2=RDKFingerprintMol(*m2,1,4,2048,4,false);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);
  TEST_ASSERT(OnBitProjSimilarity(*fp2,*fp1)[0]==1.0);

  delete m2;
  m2 = SmilesToMol("CC=O");
  delete fp2;
  fp2=RDKFingerprintMol(*m2,1,4,2048,4,false);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);
  TEST_ASSERT(OnBitProjSimilarity(*fp2,*fp1)[0]==1.0);

  delete m2;
  m2 = SmilesToMol("CCCOC");
  delete fp2;
  fp2=RDKFingerprintMol(*m2,1,4,2048,4,false);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);
  TEST_ASSERT(OnBitProjSimilarity(*fp2,*fp1)[0]==1.0);


  delete m1;
  delete m2;
  delete fp1;
  delete fp2;

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

void test3(){
  BOOST_LOG(rdInfoLog) <<"testing auto folding" << std::endl;

  RWMol *m = SmilesToMol("CCCOC");

  ExplicitBitVect *fp1,*fp2;
  fp2=RDKFingerprintMol(*m,1,4,2048,4,false,
			     0.3,256);
  TEST_ASSERT(fp2->getNumBits()==256);


  delete m;
  delete fp2;
  m=SmilesToMol("CN(C)Cc1n-2c(nn1)CN=C(c1ccccc1)c1cc(Cl)ccc12");
  fp1=RDKFingerprintMol(*m,1,4,2048,4,false);
  TEST_ASSERT(fp1->getNumBits()==2048);
  fp2=RDKFingerprintMol(*m,1,4,2048,4,false,0.3,256);  
  TEST_ASSERT(fp2->getNumBits()<fp1->getNumBits());
  
  delete m;
  delete fp1;
  delete fp2;
  BOOST_LOG(rdInfoLog) <<"done" << std::endl;

}

void test1alg2(){
  BOOST_LOG(rdInfoLog) <<"testing basics alg2" << std::endl;

  std::string smi = "C1=CC=CC=C1";
  RWMol *m1 = SmilesToMol(smi);
  TEST_ASSERT(m1->getNumAtoms()==6);
  ExplicitBitVect *fp1=RDKFingerprintMol(*m1);
  ExplicitBitVect *fp2=RDKFingerprintMol(*m1);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);
  
  smi = "C1=CC=CC=N1";
  RWMol *m2 = SmilesToMol(smi);
  delete fp2;
  fp2=RDKFingerprintMol(*m2);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);

  delete m1;
  delete m2;
  delete fp1;
  delete fp2;
  BOOST_LOG(rdInfoLog) <<"done" << std::endl;
}

void test2alg2(){
  BOOST_LOG(rdInfoLog) <<"testing subgraph invariants alg2" << std::endl;

  std::string smi = "CC(=O)COC";
  RWMol *m1 = SmilesToMol(smi);
  TEST_ASSERT(m1->getNumAtoms()==6);
  BOOST_LOG(rdInfoLog) <<"--------------------  fp1 " << std::endl;
  ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,4,2048,4,false);
  BOOST_LOG(rdInfoLog) <<"--------------------  fp2 " << std::endl;
  ExplicitBitVect *fp2=RDKFingerprintMol(*m1,1,4,2048,4,false);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);

  RWMol *m2 = SmilesToMol("CC");
  delete fp2;
  BOOST_LOG(rdInfoLog) <<"--------------------  fp2 " << std::endl;
  fp2=RDKFingerprintMol(*m2,1,4,2048,4,false);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);
  TEST_ASSERT(OnBitProjSimilarity(*fp2,*fp1)[0]==1.0);

  delete m2;
  m2 = SmilesToMol("CC=O");
  delete fp2;
  fp2=RDKFingerprintMol(*m2,1,4,2048,4,false);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);
  TEST_ASSERT(OnBitProjSimilarity(*fp2,*fp1)[0]==1.0);

  delete m2;
  m2 = SmilesToMol("CCCOC");
  delete fp2;
  fp2=RDKFingerprintMol(*m2,1,4,2048,4,false);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
  TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);
  TEST_ASSERT(OnBitProjSimilarity(*fp2,*fp1)[0]==1.0);


  delete m1;
  delete m2;
  delete fp1;
  delete fp2;

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

void test4Trends(){
  BOOST_LOG(rdInfoLog) <<"testing similarity trends" << std::endl;

  double sim1,sim2;
  RWMol *m;
  ExplicitBitVect *fp1,*fp2;
  
  m = SmilesToMol("CCC");
  fp1=RDKFingerprintMol(*m);
  delete m;
  m = SmilesToMol("C1CC1");
  fp2=RDKFingerprintMol(*m);
  sim1=TanimotoSimilarity(*fp1,*fp2);

  delete m;
  m = SmilesToMol("CCCC");
  delete fp1;
  fp1=RDKFingerprintMol(*m);
  delete m;
  m = SmilesToMol("C1CCC1");
  delete fp2;
  fp2=RDKFingerprintMol(*m);
  sim2=TanimotoSimilarity(*fp1,*fp2);
  TEST_ASSERT(sim2>sim1);
  sim2=sim1;

  delete m;
  m = SmilesToMol("CCCCC");
  delete fp1;
  fp1=RDKFingerprintMol(*m);
  delete m;
  m = SmilesToMol("C1CCCC1");
  delete fp2;
  fp2=RDKFingerprintMol(*m);
  sim2=TanimotoSimilarity(*fp1,*fp2);
  TEST_ASSERT(sim2>sim1);
  sim2=sim1;

  delete m;
  m = SmilesToMol("CCCCCC");
  delete fp1;
  fp1=RDKFingerprintMol(*m);
  delete m;
  m = SmilesToMol("C1CCCCC1");
  delete fp2;
  fp2=RDKFingerprintMol(*m);
  sim2=TanimotoSimilarity(*fp1,*fp2);
  TEST_ASSERT(sim2>sim1);
  sim2=sim1;

  delete m;
  m = SmilesToMol("CCCCCCC");
  delete fp1;
  fp1=RDKFingerprintMol(*m);
  delete m;
  m = SmilesToMol("C1CCCCCC1");
  delete fp2;
  fp2=RDKFingerprintMol(*m);
  sim2=TanimotoSimilarity(*fp1,*fp2);
  TEST_ASSERT(sim2>sim1);
  sim2=sim1;


  delete m;
  delete fp1;
  delete fp2;

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


void test5BackwardsCompatibility(){
  BOOST_LOG(rdInfoLog) <<"testing backwards compatibility of fingerprints" << std::endl;

  RWMol *m;
  ExplicitBitVect *fp1;
  
  m = SmilesToMol("CC");
  fp1=RDKFingerprintMol(*m,1,7,2048,4);
  TEST_ASSERT(fp1->getNumOnBits()==4);
#if BOOST_VERSION/100 < 1040
  // bug fixes in the uniform_int<> distribution in version 1.40
  // necessitate this
  TEST_ASSERT((*fp1)[951]);
  TEST_ASSERT((*fp1)[961]);
  TEST_ASSERT((*fp1)[1436]);
  TEST_ASSERT((*fp1)[1590]);
#else
  TEST_ASSERT((*fp1)[419]);
  TEST_ASSERT((*fp1)[718]);
  TEST_ASSERT((*fp1)[1499]);
  TEST_ASSERT((*fp1)[1504]);
#endif
  delete fp1;

  delete m;

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

void test1Layers(){
  BOOST_LOG(rdInfoLog) <<"testing basics layered fps" << std::endl;
#if 1
  {
    RWMol *m1 = SmilesToMol("C1=CC=CC=C1");
    RWMol *m2 = SmilesToMol("C1=CC=CC=N1");
    RWMol *m3 = SmilesToMol("C1CCCCC1");
    RWMol *m4 = SmilesToMol("C1CCC1");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m1);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);
  
    delete fp2;
    fp2=LayeredFingerprintMol(*m2);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);

    ExplicitBitVect *fp3=LayeredFingerprintMol(*m3);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp3)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp3)>0.0);

    ExplicitBitVect *fp4=LayeredFingerprintMol(*m4);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp4)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp4)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp3,*fp4)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp3,*fp4)>0.0);

    delete fp1;delete fp2;delete fp3;delete fp4;
    delete m1;delete m2;delete m3;delete m4;
  }
#endif
  {
    RWMol *m1 = SmilesToMol("C1=CC=CC=C1");
    RWMol *m2 = SmilesToMol("C1=CC=CC=N1");
    RWMol *m3 = SmilesToMol("C1CCCCC1");
    RWMol *m4 = SmilesToMol("CCCCCC");
    unsigned int layers=0x1;
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,layers,1,5);

    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);

    ExplicitBitVect *fp3=LayeredFingerprintMol(*m3,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)==1.0);

    ExplicitBitVect *fp4=LayeredFingerprintMol(*m4,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)==1.0);

    delete fp1;delete fp2;delete fp3;delete fp4;
    delete m1;delete m2;delete m3;delete m4;
  }

  {
    RWMol *m1 = SmilesToMol("C1=CC=CC=C1");
    RWMol *m2 = SmilesToMol("C1=CC=CC=N1");
    RWMol *m3 = SmilesToMol("C1CCCCC1");
    RWMol *m4 = SmilesToMol("CCCCCC");
    unsigned int layers=0x3;
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,layers,1,5);

    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);

    ExplicitBitVect *fp3=LayeredFingerprintMol(*m3,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)==1.0);

    ExplicitBitVect *fp4=LayeredFingerprintMol(*m4,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)<=1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp3,*fp4)==1.0);

    delete fp1;delete fp2;delete fp3;delete fp4;
    delete m1;delete m2;delete m3;delete m4;
  }

  {
    RWMol *m1 = SmilesToMol("C1=CC=CC=C1");
    RWMol *m2 = SmilesToMol("C1=CC=CC=N1");
    RWMol *m3 = SmilesToMol("C1CCCCC1");
    RWMol *m4 = SmilesToMol("CCCCCC");
    unsigned int layers=0x7;
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,layers,1,5);

    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);

    ExplicitBitVect *fp3=LayeredFingerprintMol(*m3,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)==1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp3)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp3)>0.0);

    ExplicitBitVect *fp4=LayeredFingerprintMol(*m4,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)==1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp4)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp4)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp3,*fp4)==1.0);

    delete fp1;delete fp2;delete fp3;delete fp4;
    delete m1;delete m2;delete m3;delete m4;
  }

  {
    RWMol *m1 = SmilesToMol("c1ccccc1");
    RWMol *m2 = SmilesToMol("C1CCCCC1");
    RWMol *m3 = SmilesToMol("CCCCCC");
    RWMol *m4 = SmilesToMol("C1CCCCC1");
    unsigned int layers=0xF;  // add the "in ring" bit
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,layers,1,5);

    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);

    ExplicitBitVect *fp3=LayeredFingerprintMol(*m3,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp3)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp3)>0.0);

    ExplicitBitVect *fp4=LayeredFingerprintMol(*m4,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)==1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp4)==1.0);

    delete fp1;delete fp2;delete fp3;delete fp4;
    delete m1;delete m2;delete m3;delete m4;
  }

  {
    RWMol *m1 = SmilesToMol("C1=CC=CC=C1");
    RWMol *m2 = SmilesToMol("C1CCCCC1");
    RWMol *m3 = SmilesToMol("CCCCCC");
    RWMol *m4 = SmilesToMol("C1CCCCCC1");
    unsigned int layers=0x1F;  // add the ring size bit
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,layers,1,5);

    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);

    ExplicitBitVect *fp3=LayeredFingerprintMol(*m3,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp3)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp3)>0.0);

    ExplicitBitVect *fp4=LayeredFingerprintMol(*m4,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp4)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp4)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp2,*fp4)>0.0);
    TEST_ASSERT(TanimotoSimilarity(*fp3,*fp4)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp3,*fp4)>0.0);

    delete fp1;delete fp2;delete fp3;delete fp4;
    delete m1;delete m2;delete m3;delete m4;
  }

  {
    RWMol *m1 = SmilesToMol("Cc1ncccc1");
    RWMol *m2 = SmilesToMol("Cn1ccc2nn(C)c(=O)c-2c1C");
    unsigned int layers=0x7;
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,layers,1,5);

    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,layers,1,5);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)>0.0);
    TEST_ASSERT(((*fp1)&(*fp2))==(*fp1));

    delete fp1;delete fp2;
    delete m1;delete m2;
  }

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


void test2Layers(){
  BOOST_LOG(rdInfoLog) <<"testing advanced layered fps" << std::endl;
  {
    std::vector<unsigned int> atomCounts;
    RWMol *m1 = SmilesToMol("CC(C)C");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m1);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);
  
    atomCounts.clear();
    atomCounts.resize(m1->getNumAtoms());
    for(unsigned int i=0;i<m1->getNumAtoms();++i) atomCounts[i]=0;

    delete fp2;
    fp2=LayeredFingerprintMol(*m1,0xFFFFFFFF,1,7,2048,&atomCounts);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);
    TEST_ASSERT(atomCounts[0]==4);
    TEST_ASSERT(atomCounts[1]==7);
    TEST_ASSERT(atomCounts[2]==4);
    TEST_ASSERT(atomCounts[3]==4);

    delete fp2;
    fp2=LayeredFingerprintMol(*m1,0xFFFFFFFF,1,7,2048,&atomCounts);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)==1.0);
    TEST_ASSERT(atomCounts[0]==8);
    TEST_ASSERT(atomCounts[1]==14);
    TEST_ASSERT(atomCounts[2]==8);
    TEST_ASSERT(atomCounts[3]==8);


    delete fp1;delete fp2;
    delete m1;
  }


  {
    std::vector<unsigned int> atomCounts;
    RWMol *m1 = SmilesToMol("CC(C)C");
    RWMol *m2 = SmilesToMol("CCC");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp2)<1.0);
  
    atomCounts.clear();
    atomCounts.resize(m1->getNumAtoms());
    for(unsigned int i=0;i<m1->getNumAtoms();++i) atomCounts[i]=0;

    ExplicitBitVect *fp3=LayeredFingerprintMol(*m1,0xFFFFFFFF,1,7,2048,&atomCounts,fp2);
    TEST_ASSERT(TanimotoSimilarity(*fp1,*fp3)<1.0);
    TEST_ASSERT(atomCounts[0]==3);
    TEST_ASSERT(atomCounts[1]==6);
    TEST_ASSERT(atomCounts[2]==3);
    TEST_ASSERT(atomCounts[3]==3);

    delete fp1;delete fp2;delete fp3;
    delete m1;delete m2;
  }

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

void test3Layers(){
  BOOST_LOG(rdInfoLog) <<"testing layered fps and queries" << std::endl;
  {
    RWMol *m1 = SmilesToMol("CC(C)C");
    RWMol *m2 = SmartsToMol("CC(C)C");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,0x7,1,5,256);
    TEST_ASSERT(fp2->getNumOnBits());
    
    ExplicitBitVect fp3=(*fp1)&(*fp2);
#if 0
    std::cerr<<BitVectToText(*fp1)<<std::endl;
    std::cerr<<"---"<<std::endl;
    std::cerr<<BitVectToText(*fp2)<<std::endl;
    std::cerr<<BitVectToText(fp3)<<std::endl;
#endif
    TEST_ASSERT(fp3==(*fp2));
  
    delete fp1;delete fp2;
    delete m1;delete m2;
  }
 
  {
    RWMol *m1 = SmilesToMol("CC(C)C");
    RWMol *m2 = SmartsToMol("C-C(-C)-C");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,0x7,1,5,256);
    TEST_ASSERT(fp2->getNumOnBits());
    
    ExplicitBitVect fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));
  
    delete fp1;delete fp2;
    delete m1;delete m2;
  }
 
  {
    RWMol *m1 = SmilesToMol("CC(=C)C");
    RWMol *m2 = SmartsToMol("C-C(-C)-C");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,0x7,1,5,256);
    TEST_ASSERT(fp2->getNumOnBits());
    
    ExplicitBitVect fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3!=(*fp2));
    TEST_ASSERT(fp3!=(*fp1));
  
    delete fp1;delete fp2;
    delete m1;delete m2;
  }
 
  {
    RWMol *m1 = SmilesToMol("CC(C)C");
    RWMol *m2 = SmartsToMol("CC([C,N])C");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,0x7,1,5,256);
    TEST_ASSERT(fp2->getNumOnBits());
    
    ExplicitBitVect fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));
  
    delete fp1;delete fp2;
    delete m1;delete m2;
  }

  {
    RWMol *m1 = SmilesToMol("CC(C)C");
    RWMol *m2 = SmartsToMol("CC([!C])C");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,0x7,1,5,256);
    TEST_ASSERT(fp2->getNumOnBits());
    
    // the query says "!C", but we still match in the fp...
    ExplicitBitVect fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));


    // of course we better match if the thing really isn't a C:
    delete fp1;delete m1;
    m1 = SmilesToMol("CC(O)C");
    fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));
  
    delete fp1;delete fp2;
    delete m1;delete m2;
  }

  {
    RWMol *m1 = SmilesToMol("CC(O)C");
    RWMol *m2 = SmartsToMol("CC([C,N])C");

    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,0x7,1,5,256);
    TEST_ASSERT(fp2->getNumOnBits());
    
    ExplicitBitVect fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));
  
    delete fp1;delete fp2;
    delete m1;delete m2;
  }
 
  {
    RWMol *m1 = SmilesToMol("c1ccccc1");
    RWMol *m2 = SmartsToMol("cccc");
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,0x7,1,5,256);
    TEST_ASSERT(fp2->getNumOnBits());
    
    ExplicitBitVect fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));

    delete fp1;delete m1;
    // somewhat counter-intuitive result here, but this happens
    // because the aromaticity does not factor into the
    // calculation:
    m1 = SmilesToMol("C1CCCCC1");
    fp1=LayeredFingerprintMol(*m1,0x7,1,5,256);
    fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));
    
    delete fp1;delete fp2;
    delete m1;delete m2;
  }
 
  {
    RWMol *m1 = SmilesToMol("c1ccccc1");
    RWMol *m2 = SmartsToMol("c:c:c");
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0xFFFF,1,5,512);
    ExplicitBitVect *fp2=LayeredFingerprintMol(*m2,0x5,1,5,512);
    TEST_ASSERT(fp2->getNumOnBits());
    ExplicitBitVect fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));

    delete fp1;delete m1;
    m1 = SmilesToMol("C1CCCCC1");
    fp1=LayeredFingerprintMol(*m1,0xFFFF,1,5,512);
    fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));
    delete fp2;
    fp2=LayeredFingerprintMol(*m2,0x7,1,5,512);
    fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));

    delete fp2;
    fp2=LayeredFingerprintMol(*m2,0x25,1,5,512);
    fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3!=(*fp2));

    delete fp2;
    fp2=LayeredFingerprintMol(*m2,0x7,1,5,512);
    delete fp1;delete m1;
    // atom type information is factored in:
    m1 = SmilesToMol("c1ncncn1");
    fp1=LayeredFingerprintMol(*m1,0xFFFF,1,5,512);
    fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3!=(*fp2));

    delete fp2;delete m2;
    // but queries switch us back to generic types, so we match again:
    m2 = SmartsToMol("[C,N]:[C,N]:[C,N]");
    fp2=LayeredFingerprintMol(*m2,0x7,1,5,512);
    TEST_ASSERT(fp2->getNumOnBits());
    fp3=(*fp1)&(*fp2);
    TEST_ASSERT(fp3==(*fp2));
    
    delete fp1;delete fp2;
    delete m1;delete m2;
  }
 
 
 BOOST_LOG(rdInfoLog) <<"done" << std::endl;
}


void test1MorganFPs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Morgan Fingerprints." << std::endl;

  {
    ROMol *mol;
    SparseIntVect<boost::uint32_t> *fp;

    mol = SmilesToMol("CCCCC");
    fp = MorganFingerprints::getFingerprint(*mol,0);
    TEST_ASSERT(fp->getNonzeroElements().size()==2);
    delete fp;

    fp = MorganFingerprints::getFingerprint(*mol,0,0,0,false,true,false);
    TEST_ASSERT(fp->getNonzeroElements().size()==2);
    for(SparseIntVect<boost::uint32_t>::StorageType::const_iterator iter=fp->getNonzeroElements().begin();
        iter!=fp->getNonzeroElements().end();++iter){
      TEST_ASSERT(iter->second==1); // check that count == 1
      ++iter;
    }
    delete fp;

    fp = MorganFingerprints::getHashedFingerprint(*mol,0);
    TEST_ASSERT(fp->getNonzeroElements().size()==2);
    delete fp;

    fp = MorganFingerprints::getFingerprint(*mol,1);
    TEST_ASSERT(fp->getNonzeroElements().size()==5);
    delete fp;
    fp = MorganFingerprints::getHashedFingerprint(*mol,1);
    TEST_ASSERT(fp->getNonzeroElements().size()==5);
    delete fp;

    fp = MorganFingerprints::getFingerprint(*mol,2);
    TEST_ASSERT(fp->getNonzeroElements().size()==7);
    delete fp;

    fp = MorganFingerprints::getFingerprint(*mol,3);
    TEST_ASSERT(fp->getNonzeroElements().size()==7);
    delete fp;

  
    delete mol;
  }
  {
    ROMol *mol;
    SparseIntVect<boost::uint32_t> *fp;

    mol = SmilesToMol("O=C(O)CC1CC1");
    fp = MorganFingerprints::getFingerprint(*mol,0);
    TEST_ASSERT(fp->getNonzeroElements().size()==6);
    delete fp;
    fp = MorganFingerprints::getFingerprint(*mol,1);
    TEST_ASSERT(fp->getNonzeroElements().size()==12);
    delete fp;
    fp = MorganFingerprints::getFingerprint(*mol,2);
    TEST_ASSERT(fp->getNonzeroElements().size()==16);
    delete fp;
    fp = MorganFingerprints::getFingerprint(*mol,3);
    TEST_ASSERT(fp->getNonzeroElements().size()==17);
    delete fp;

    delete mol;
  }

  {
    // test that the results aren't order dependent, i.e. that we're
    // "canonicalizing" the fps correctly
    ROMol *mol,*mol2;
    SparseIntVect<boost::uint32_t> *fp,*fp2;

    mol = SmilesToMol("O=C(O)CC1CC1");
    mol2 = SmilesToMol("OC(=O)CC1CC1");
    fp = MorganFingerprints::getFingerprint(*mol,0);
    fp2 = MorganFingerprints::getFingerprint(*mol2,0);
    TEST_ASSERT(fp->getNonzeroElements().size()==6);
    TEST_ASSERT(fp2->getNonzeroElements().size()==6);
    TEST_ASSERT(*fp==*fp2);
    delete fp;
    delete fp2;

    fp = MorganFingerprints::getFingerprint(*mol,1);
    fp2 = MorganFingerprints::getFingerprint(*mol2,1);
    TEST_ASSERT(fp->getNonzeroElements().size()==12);
    TEST_ASSERT(fp2->getNonzeroElements().size()==12);
    TEST_ASSERT(*fp==*fp2);
    delete fp;
    delete fp2;

    fp = MorganFingerprints::getFingerprint(*mol,2);
    fp2 = MorganFingerprints::getFingerprint(*mol2,2);
    TEST_ASSERT(fp->getNonzeroElements().size()==16);
    TEST_ASSERT(fp2->getNonzeroElements().size()==16);
    TEST_ASSERT(*fp==*fp2);
    delete fp;
    delete fp2;

    fp = MorganFingerprints::getFingerprint(*mol,3);
    fp2 = MorganFingerprints::getFingerprint(*mol2,3);
    TEST_ASSERT(fp->getNonzeroElements().size()==17);
    TEST_ASSERT(fp2->getNonzeroElements().size()==17);
    TEST_ASSERT(*fp==*fp2);
    delete fp;
    delete fp2;

    delete mol;
    delete mol2;
  }

  {
    // symmetry test:
    ROMol *mol;
    SparseIntVect<boost::uint32_t> *fp;

    mol = SmilesToMol("OCCCCO");
    fp = MorganFingerprints::getFingerprint(*mol,2);
    TEST_ASSERT(fp->getNonzeroElements().size()==7);
    SparseIntVect<boost::uint32_t>::StorageType::const_iterator iter;
    for(iter=fp->getNonzeroElements().begin();
        iter!=fp->getNonzeroElements().end();++iter){
      TEST_ASSERT(iter->second==2 || iter->second==4);
    }
    
    delete fp;
    delete mol;
  }

  {
    // chirality test:
    ROMol *mol;
    SparseIntVect<boost::uint32_t> *fp;

    mol = SmilesToMol("CC(F)(Cl)C(F)(Cl)C");
    fp = MorganFingerprints::getFingerprint(*mol,0);
    TEST_ASSERT(fp->getNonzeroElements().size()==4);
    delete fp;
    fp = MorganFingerprints::getFingerprint(*mol,1);
    TEST_ASSERT(fp->getNonzeroElements().size()==8);
    delete mol;
    delete fp;

    mol = SmilesToMol("CC(F)(Cl)[C@](F)(Cl)C");
    fp = MorganFingerprints::getFingerprint(*mol,0);
    TEST_ASSERT(fp->getNonzeroElements().size()==4);
    delete fp;
    fp = MorganFingerprints::getFingerprint(*mol,1);
    TEST_ASSERT(fp->getNonzeroElements().size()==8);
    delete fp;
    fp = MorganFingerprints::getFingerprint(*mol,0,0,0,true);
    TEST_ASSERT(fp->getNonzeroElements().size()==4);
    delete fp;
    fp = MorganFingerprints::getFingerprint(*mol,1,0,0,true);
    TEST_ASSERT(fp->getNonzeroElements().size()==9);
    delete fp;
    delete mol;
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void test2MorganFPsFromAtoms(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Morgan Fingerprints using fromAtoms argument." << std::endl;

  {
    ROMol *mol;
    SparseIntVect<boost::uint32_t> *fp;
    std::vector<boost::uint32_t> atoms;
    atoms.push_back(0);
    
    mol = SmilesToMol("CCCCC");
    fp = MorganFingerprints::getFingerprint(*mol,0);
    TEST_ASSERT(fp->getNonzeroElements().size()==2);
    delete fp;

    fp = MorganFingerprints::getFingerprint(*mol,0,(std::vector<boost::uint32_t> *)NULL,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==1);
    delete fp;
  
    fp = MorganFingerprints::getFingerprint(*mol,1,(std::vector<boost::uint32_t> *)NULL,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==2);
    delete fp;
  
    // tests issue 3415636
    fp = MorganFingerprints::getFingerprint(*mol,2,(std::vector<boost::uint32_t> *)NULL,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==3);
    delete fp;
  
    delete mol;
  }

  {
    ROMol *mol;
    SparseIntVect<boost::uint32_t> *fp;
    std::vector<boost::uint32_t> atoms;
    
    mol = SmilesToMol("CCCCC");
    fp = MorganFingerprints::getFingerprint(*mol,0,(std::vector<boost::uint32_t> *)0,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==0);
    delete fp;
  
    fp = MorganFingerprints::getFingerprint(*mol,1,(std::vector<boost::uint32_t> *)0,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==0);
    delete fp;
  
    delete mol;
  }

  {
    ROMol *mol;
    SparseIntVect<boost::uint32_t> *fp;
    std::vector<boost::uint32_t> atoms;
    atoms.push_back(0);
    
    mol = SmilesToMol("C(CC)CO");

    fp = MorganFingerprints::getFingerprint(*mol,0,(std::vector<boost::uint32_t> *)0,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==1);
    delete fp;
  
    fp = MorganFingerprints::getFingerprint(*mol,1,(std::vector<boost::uint32_t> *)0,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==2);
    delete fp;
  
    fp = MorganFingerprints::getFingerprint(*mol,2,(std::vector<boost::uint32_t> *)0,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==3);
    delete fp;
  
    // tests issue 3415636
    fp = MorganFingerprints::getFingerprint(*mol,3,(std::vector<boost::uint32_t> *)0,&atoms);
    TEST_ASSERT(fp->getNonzeroElements().size()==3);
    delete fp;
  
    delete mol;
  }
  
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}


void test3MorganFPs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Morgan Fingerprints as bit vects." << std::endl;

  {
    ROMol *mol;
    ExplicitBitVect *fp;

    mol = SmilesToMol("CCCCC");
    fp = MorganFingerprints::getFingerprintAsBitVect(*mol,0,2048);
    TEST_ASSERT(fp->getNumOnBits()==2);
    delete fp;
    fp = MorganFingerprints::getFingerprintAsBitVect(*mol,1,2048);
    TEST_ASSERT(fp->getNumOnBits()==5);
    delete fp;
    fp = MorganFingerprints::getFingerprintAsBitVect(*mol,2,2048);
    TEST_ASSERT(fp->getNumOnBits()==7);
    delete fp;
    fp = MorganFingerprints::getFingerprintAsBitVect(*mol,3,2048);
    TEST_ASSERT(fp->getNumOnBits()==7);
    delete fp;
  
  
    delete mol;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void test4MorganFPs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Morgan Fingerprints with feature invariants." << std::endl;

  {
    ROMol *mol;
    mol = SmilesToMol("Cc1ccccc1");
    TEST_ASSERT(mol);
    std::vector<boost::uint32_t> invars(mol->getNumAtoms());
    MorganFingerprints::getFeatureInvariants(*mol,invars);
    TEST_ASSERT(invars[0]==0);
    TEST_ASSERT(invars[1]!=0);
    TEST_ASSERT(invars[1]==invars[2]);
    TEST_ASSERT(invars[1]==invars[3]);
    TEST_ASSERT(invars[1]==invars[4]);
    TEST_ASSERT(invars[1]==invars[5]);
    TEST_ASSERT(invars[1]==invars[6]);
    delete mol;
  }
  {
    ROMol *mol;
    mol = SmilesToMol("FCCCl");
    TEST_ASSERT(mol);
    std::vector<boost::uint32_t> invars(mol->getNumAtoms());
    MorganFingerprints::getFeatureInvariants(*mol,invars);
    TEST_ASSERT(invars[1]==invars[2]);
    TEST_ASSERT(invars[1]==0);
    TEST_ASSERT(invars[0]==invars[3]);
    TEST_ASSERT(invars[0]!=0);
    delete mol;
  }
  {
    ROMol *mol;
    mol = SmilesToMol("Cc1ncccc1O");
    TEST_ASSERT(mol);
    std::vector<boost::uint32_t> invars(mol->getNumAtoms());

    std::vector<const ROMol *> patterns(2);
    RWMol *p;
    p=SmartsToMol("[A]");
    patterns[0]=static_cast<const ROMol *>(p);
    p=SmartsToMol("[a]");
    patterns[1]=static_cast<const ROMol *>(p);
    
    MorganFingerprints::getFeatureInvariants(*mol,invars,&patterns);
    TEST_ASSERT(invars[0]!=0);
    TEST_ASSERT(invars[1]!=0);
    TEST_ASSERT(invars[0]!=invars[1]);
    TEST_ASSERT(invars[1]==invars[2]);
    TEST_ASSERT(invars[0]==invars[7]);
    delete mol;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void test5MorganFPs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test additional Morgan fingerprints options." << std::endl;

  {
    ROMol *m1,*m2;
    ExplicitBitVect *fp1,*fp2;
    std::vector<boost::uint32_t> invars(3);
    invars[0]=1;
    invars[1]=1;
    invars[2]=1;

    m1 = SmilesToMol("CCC");
    TEST_ASSERT(m1);
    m2 = SmilesToMol("CC=C");
    TEST_ASSERT(m2);

    fp1 = MorganFingerprints::getFingerprintAsBitVect(*m1,2,2048,&invars,0,false,true);
    invars[0]=1;
    invars[1]=1;
    invars[2]=1;
    fp2 = MorganFingerprints::getFingerprintAsBitVect(*m2,2,2048,&invars,0,false,true);
    TEST_ASSERT((*fp1)!=(*fp2));
    delete fp1;
    delete fp2;

    invars[0]=1;
    invars[1]=1;
    invars[2]=1;
    fp1 = MorganFingerprints::getFingerprintAsBitVect(*m1,2,2048,&invars,0,false,false);
    invars[0]=1;
    invars[1]=1;
    invars[2]=1;
    fp2 = MorganFingerprints::getFingerprintAsBitVect(*m2,2,2048,&invars,0,false,false);
    TEST_ASSERT((*fp1)==(*fp2));
    delete fp1;
    delete fp2;

    delete m1;
    delete m2;
  }

  {
    ROMol *m1,*m2,*m3;
    ExplicitBitVect *fp1,*fp2,*fp3;

    m1 = SmilesToMol("C[C@H](F)Cl");
    TEST_ASSERT(m1);
    m2 = SmilesToMol("C[C@@H](F)Cl");
    TEST_ASSERT(m2);
    m3 = SmilesToMol("CC(F)Cl");
    TEST_ASSERT(m3);

    fp1 = MorganFingerprints::getFingerprintAsBitVect(*m1,2,2048,0,0,false,true);
    fp2 = MorganFingerprints::getFingerprintAsBitVect(*m2,2,2048,0,0,false,true);
    fp3 = MorganFingerprints::getFingerprintAsBitVect(*m3,2,2048,0,0,false,true);
    TEST_ASSERT((*fp1)==(*fp2));
    TEST_ASSERT((*fp1)==(*fp3));
    TEST_ASSERT((*fp2)==(*fp3));
    delete fp1;
    delete fp2;
    delete fp3;

    fp1 = MorganFingerprints::getFingerprintAsBitVect(*m1,2,2048,0,0,true,true);
    fp2 = MorganFingerprints::getFingerprintAsBitVect(*m2,2,2048,0,0,true,true);
    fp3 = MorganFingerprints::getFingerprintAsBitVect(*m3,2,2048,0,0,true,true);
    TEST_ASSERT((*fp1)!=(*fp2));
    TEST_ASSERT((*fp1)!=(*fp3));
    TEST_ASSERT((*fp2)!=(*fp3));
    delete fp1;
    delete fp2;
    delete fp3;

    delete m1;
    delete m2;
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testIssue2875658(){
  BOOST_LOG(rdInfoLog) <<"testing issue 2875658" << std::endl;

  RWMol *m;
  ExplicitBitVect *fp1,*fp2;
  
  m = SmilesToMol("c1ccccc1");
  fp1=RDKFingerprintMol(*m,1,7,2048,4);
  delete m;
  m = SmilesToMol("c1cccnc1");
  fp2=RDKFingerprintMol(*m,1,7,2048,4);
  delete m;

#if BOOST_VERSION/100 >= 1040
  // bug fixes in the uniform_int<> distribution in version 1.40
  // necessitate this
  TEST_ASSERT(fp1->getNumOnBits()==24);
  TEST_ASSERT((*fp1)[11]);
  TEST_ASSERT((*fp1)[857]);
  TEST_ASSERT((*fp1)[1786]);
  TEST_ASSERT((*fp1)[2020]);

  TEST_ASSERT(fp2->getNumOnBits()==64);
  TEST_ASSERT((*fp2)[11]);
  TEST_ASSERT((*fp2)[179]);
  TEST_ASSERT((*fp2)[1878]);
  TEST_ASSERT((*fp2)[2020]);
#else
  TEST_ASSERT(fp1->getNumOnBits()==24);
  TEST_ASSERT((*fp1)[23]);
  TEST_ASSERT((*fp1)[434]);
  TEST_ASSERT((*fp1)[1445]);
  TEST_ASSERT((*fp1)[2031]);

  TEST_ASSERT(fp2->getNumOnBits()==62);
  TEST_ASSERT((*fp2)[23]);
  TEST_ASSERT((*fp2)[173]);
  TEST_ASSERT((*fp2)[1847]);
  TEST_ASSERT((*fp2)[1975]);
#endif
  delete fp1;
  delete fp2;
}

void testAtomCodes(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Atom Codes." << std::endl;

  ROMol *mol;
  boost::uint32_t tgt;
  mol = SmilesToMol("C=C");
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(0))==AtomPairs::getAtomCode(mol->getAtomWithIdx(1)));
  tgt = 1 | (1 | 1<<AtomPairs::numPiBits)<<AtomPairs::numBranchBits;
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(0))==tgt);
  tgt = 1<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(0),1)==tgt);

  delete mol;
  mol = SmilesToMol("C#CO");
  tgt = 1 | 2<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(0))==tgt);
  tgt = 2 | 2<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(1))==tgt);
  tgt = 1 | 0<<AtomPairs::numBranchBits | 3<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(2))==tgt);

  delete mol;
  mol = SmilesToMol("CC(O)C(O)(O)C");
  tgt = 1 | 0<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(1),2)==tgt);
  tgt = 2 | 0<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(3),2)==tgt);
  
  delete mol;
  mol = SmilesToMol("C=CC(=O)O");
  tgt = 0 | 0<<AtomPairs::numBranchBits | 3<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(4),1)==tgt);
  tgt = 3 | 1<<AtomPairs::numBranchBits | 1<<(AtomPairs::numBranchBits+AtomPairs::numPiBits);
  TEST_ASSERT(AtomPairs::getAtomCode(mol->getAtomWithIdx(2))==tgt);


  delete mol;
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testAtomPairs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Atom Pairs." << std::endl;

  ROMol *mol;
  SparseIntVect<boost::int32_t> *fp;
  boost::uint32_t tgt;
  boost::uint32_t c1,c2,c3;

  mol = SmilesToMol("CCCCC");
  c1=AtomPairs::getAtomCode(mol->getAtomWithIdx(0));
  c2=AtomPairs::getAtomCode(mol->getAtomWithIdx(1));
  c3=AtomPairs::getAtomCode(mol->getAtomWithIdx(2));
  tgt = 1 | (std::min(c1,c2) | std::max(c1,c2)<<AtomPairs::codeSize)<< AtomPairs::numPathBits;
  TEST_ASSERT(AtomPairs::getAtomPairCode(c1,c2,1)==tgt);
  TEST_ASSERT(AtomPairs::getAtomPairCode(c2,c1,1)==tgt);
  tgt = 2 | (std::min(c1,c3) | std::max(c1,c3)<<AtomPairs::codeSize)<< AtomPairs::numPathBits;
  TEST_ASSERT(AtomPairs::getAtomPairCode(c1,c3,2)==tgt);
  TEST_ASSERT(AtomPairs::getAtomPairCode(c3,c1,2)==tgt);

  delete mol;
  mol = SmilesToMol("CCC");
  fp=AtomPairs::getAtomPairFingerprint(*mol);
  TEST_ASSERT(fp->getTotalVal()==3);
  TEST_ASSERT(fp->getNonzeroElements().size()==2);

  c1=AtomPairs::getAtomCode(mol->getAtomWithIdx(0));
  c2=AtomPairs::getAtomCode(mol->getAtomWithIdx(1));
  c3=AtomPairs::getAtomCode(mol->getAtomWithIdx(2));
  TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c1,c2,1))==2);
  TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c1,c3,2))==1);
  
  delete mol;
  delete fp;
  mol = SmilesToMol("CC=O.Cl");
  fp=AtomPairs::getAtomPairFingerprint(*mol);
  TEST_ASSERT(fp->getTotalVal()==3);
  TEST_ASSERT(fp->getNonzeroElements().size()==3);

  c1=AtomPairs::getAtomCode(mol->getAtomWithIdx(0));
  c2=AtomPairs::getAtomCode(mol->getAtomWithIdx(1));
  c3=AtomPairs::getAtomCode(mol->getAtomWithIdx(2));
  TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c1,c2,1))==1);
  TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c1,c2,1))==1);
  TEST_ASSERT(fp->getVal(AtomPairs::getAtomPairCode(c2,c3,1))==1);
  
  delete mol;
  delete fp;
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testAtomPairs2(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Atom Pairs part 2." << std::endl;

  {
    ROMol *mol;
    SparseIntVect<boost::int32_t> *fp;

    mol = SmilesToMol("CCC");
    fp=AtomPairs::getAtomPairFingerprint(*mol,1,2);
    TEST_ASSERT(fp->getTotalVal()==3);
    TEST_ASSERT(fp->getNonzeroElements().size()==2);
  
    delete fp;
    fp=AtomPairs::getAtomPairFingerprint(*mol,2,2);
    TEST_ASSERT(fp->getTotalVal()==1);
    TEST_ASSERT(fp->getNonzeroElements().size()==1);
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testHashedAtomPairs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Hashed Atom Pairs." << std::endl;

  {
    ROMol *mol;
    mol = SmilesToMol("c1ccccc1");
    SparseIntVect<boost::int32_t> *fp1;
    fp1=AtomPairs::getHashedAtomPairFingerprint(*mol);
    SparseIntVect<boost::int32_t> *fp2;
    fp2=AtomPairs::getHashedAtomPairFingerprint(*mol);
    TEST_ASSERT(DiceSimilarity(*fp1,*fp2)==1.0);
    TEST_ASSERT(*fp1==*fp2);

    delete mol;
    delete fp2;
    mol = SmilesToMol("c1ccccn1");
    fp2=AtomPairs::getHashedAtomPairFingerprint(*mol);
    RANGE_CHECK(0.0,DiceSimilarity(*fp1,*fp2),1.0);

    delete mol;
    delete fp1;
    delete fp2;
  }

  {
    ROMol *mol;
    mol = SmilesToMol("c1ccccc1");
    SparseIntVect<boost::int32_t> *fp1;
    fp1=AtomPairs::getHashedAtomPairFingerprint(*mol,2048);
    SparseIntVect<boost::int32_t> *fp2;
    fp2=AtomPairs::getHashedAtomPairFingerprint(*mol,2048,1,3);
    TEST_ASSERT(DiceSimilarity(*fp1,*fp2)==1.0);
    TEST_ASSERT(*fp1==*fp2);

    delete fp2;
    fp2=AtomPairs::getHashedAtomPairFingerprint(*mol,2048,1,2);
    RANGE_CHECK(0.0,DiceSimilarity(*fp1,*fp2),1.0);

    delete mol;
    delete fp1;
    delete fp2;
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}


void testTorsions(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Topological Torsions." << std::endl;

  ROMol *mol;
  SparseIntVect<boost::int64_t> *fp;
  boost::uint64_t tgt;
  boost::uint64_t  c1,c2,c3,c4;
  std::vector<boost::uint32_t> codes;

  mol = SmilesToMol("CCCC");
  c1=AtomPairs::getAtomCode(mol->getAtomWithIdx(0))-1;
  c2=AtomPairs::getAtomCode(mol->getAtomWithIdx(1))-2;
  c3=AtomPairs::getAtomCode(mol->getAtomWithIdx(2))-2;
  c4=AtomPairs::getAtomCode(mol->getAtomWithIdx(3))-1;
  tgt = c1 | (c2 | (c3 | c4<<AtomPairs::codeSize)<<AtomPairs::codeSize)<<AtomPairs::codeSize;
  codes.clear();
  codes.push_back(static_cast<unsigned int>(c1));
  codes.push_back(static_cast<unsigned int>(c2));
  codes.push_back(static_cast<unsigned int>(c3));
  codes.push_back(static_cast<unsigned int>(c4));
  TEST_ASSERT(AtomPairs::getTopologicalTorsionCode(codes)==tgt);

  fp = AtomPairs::getTopologicalTorsionFingerprint(*mol);
  TEST_ASSERT(fp->getTotalVal()==1);
  TEST_ASSERT(fp->getNonzeroElements().size()==1);


  delete mol;
  delete fp;
  mol = SmilesToMol("CCCCO.Cl");
  fp=AtomPairs::getTopologicalTorsionFingerprint(*mol);
  TEST_ASSERT(fp->getTotalVal()==2);
  TEST_ASSERT(fp->getNonzeroElements().size()==2);

  delete fp;
  fp = AtomPairs::getTopologicalTorsionFingerprint(*mol,3);
  TEST_ASSERT(fp->getTotalVal()==3);
  TEST_ASSERT(fp->getNonzeroElements().size()==3);

  delete mol;
  delete fp;
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testHashedTorsions(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Hashed torsions." << std::endl;

  {
    ROMol *mol;
    mol = SmilesToMol("c1ccccc1");
    SparseIntVect<boost::int64_t> *fp1;
    fp1=AtomPairs::getHashedTopologicalTorsionFingerprint(*mol);
    SparseIntVect<boost::int64_t> *fp2;
    fp2=AtomPairs::getHashedTopologicalTorsionFingerprint(*mol);
    TEST_ASSERT(DiceSimilarity(*fp1,*fp2)==1.0);
    TEST_ASSERT(*fp1==*fp2);

    delete mol;
    delete fp2;
    mol = SmilesToMol("c1ccccn1");
    fp2=AtomPairs::getHashedTopologicalTorsionFingerprint(*mol);
    RANGE_CHECK(0.0,DiceSimilarity(*fp1,*fp2),1.0);

    delete mol;
    delete fp1;
    delete fp2;
  }

  {
    ROMol *mol;
    mol = SmilesToMol("c1ccccc1");
    SparseIntVect<boost::int64_t> *fp1;
    fp1=AtomPairs::getHashedTopologicalTorsionFingerprint(*mol,2048,6);
    SparseIntVect<boost::int64_t> *fp2;
    fp2=AtomPairs::getHashedTopologicalTorsionFingerprint(*mol,2048,6);
    TEST_ASSERT(DiceSimilarity(*fp1,*fp2)==1.0);
    TEST_ASSERT(*fp1==*fp2);

    delete mol;
    delete fp2;
    mol = SmilesToMol("c1ccccn1");
    fp2=AtomPairs::getHashedTopologicalTorsionFingerprint(*mol,2048,6);
    RANGE_CHECK(0.0,DiceSimilarity(*fp1,*fp2),1.0);

    delete mol;
    delete fp1;
    delete fp2;
  }


  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}




void testBulkTorsions(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Bulk Topological Torsions." << std::endl;

  std::string fName= getenv("RDBASE");
  fName += "/Projects/DbCLI/testData/pubchem.200.sdf";
  SDMolSupplier suppl(fName);
  while(!suppl.atEnd()){
    ROMol *mol=suppl.next();
    SparseIntVect<boost::int64_t> *fp;
    fp = AtomPairs::getTopologicalTorsionFingerprint(*mol);
    TEST_ASSERT(fp->getTotalVal()>1);
    delete mol;
    delete fp;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testRootedAtomPairs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Rooted Atom Pairs." << std::endl;

  ROMol *mol;
  SparseIntVect<boost::int32_t> *fp1,*fp2;
  std::vector<boost::uint32_t> roots;

  mol = SmilesToMol("OCCCCC");
  fp1=AtomPairs::getAtomPairFingerprint(*mol);
  SparseIntVect<boost::int32_t>::StorageType nz1=fp1->getNonzeroElements();
  TEST_ASSERT(nz1.size()>0);

  roots.push_back(0);
  fp2=AtomPairs::getAtomPairFingerprint(*mol,&roots);
  SparseIntVect<boost::int32_t>::StorageType nz2=fp2->getNonzeroElements();
  TEST_ASSERT(nz2.size()>0);
  TEST_ASSERT(nz2.size()<nz1.size());

  for(SparseIntVect<boost::int32_t>::StorageType::const_iterator bIt=nz2.begin();
      bIt!=nz2.end();++bIt){
    TEST_ASSERT(bIt->second<=fp2->getVal(bIt->first));
  }

  delete mol;
  delete fp1;
  delete fp2;

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testIgnoreAtomPairs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test ignoring atoms in Atom Pairs." << std::endl;

  {
    ROMol *mol;
    SparseIntVect<boost::int32_t> *fp1,*fp2;
    std::vector<boost::uint32_t> roots;

    mol = SmilesToMol("OCCCCC");
    fp1=AtomPairs::getAtomPairFingerprint(*mol,1,5);
    SparseIntVect<boost::int32_t>::StorageType nz1=fp1->getNonzeroElements();
    TEST_ASSERT(nz1.size()>0);

    roots.push_back(0);
    fp2=AtomPairs::getAtomPairFingerprint(*mol,1,5,0,&roots);
    SparseIntVect<boost::int32_t>::StorageType nz2=fp2->getNonzeroElements();
    TEST_ASSERT(nz2.size()==nz1.size()-5);

    for(SparseIntVect<boost::int32_t>::StorageType::const_iterator bIt=nz2.begin();
        bIt!=nz2.end();++bIt){
      TEST_ASSERT(bIt->second<=fp2->getVal(bIt->first));
    }

    delete mol;
    delete fp1;
    delete fp2;
  }
  {
    ROMol *mol;
    SparseIntVect<boost::int32_t> *fp2;
    std::vector<boost::uint32_t> roots;

    mol = SmilesToMol("OCCCCC");
    roots.push_back(0);
    fp2=AtomPairs::getAtomPairFingerprint(*mol,1,5,&roots,&roots);
    SparseIntVect<boost::int32_t>::StorageType nz2=fp2->getNonzeroElements();
    TEST_ASSERT(nz2.size()==0);

    delete mol;
    delete fp2;
  }

  {
    ROMol *mol;
    SparseIntVect<boost::int32_t> *fp1,*fp2;
    std::vector<boost::uint32_t> roots;

    mol = SmilesToMol("OCCCCC");
    fp1=AtomPairs::getHashedAtomPairFingerprint(*mol,4096,1,5);
    SparseIntVect<boost::int32_t>::StorageType nz1=fp1->getNonzeroElements();
    TEST_ASSERT(nz1.size()>0);

    roots.push_back(0);
    fp2=AtomPairs::getHashedAtomPairFingerprint(*mol,4096,1,5,0,&roots);
    SparseIntVect<boost::int32_t>::StorageType nz2=fp2->getNonzeroElements();
    TEST_ASSERT(nz2.size()<nz1.size());

    for(SparseIntVect<boost::int32_t>::StorageType::const_iterator bIt=nz2.begin();
        bIt!=nz2.end();++bIt){
      TEST_ASSERT(bIt->second<=fp2->getVal(bIt->first));
    }

    delete mol;
    delete fp1;
    delete fp2;
  }


  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}



void testRootedTorsions(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Rooted Topological Torsions." << std::endl;

  ROMol *mol;
  SparseIntVect<boost::int64_t> *fp1,*fp2;
  std::vector<boost::uint32_t> roots;


  mol = SmilesToMol("OCCCC");
  roots.push_back(0);

  fp1 = AtomPairs::getTopologicalTorsionFingerprint(*mol);
  SparseIntVect<boost::int64_t>::StorageType nz1=fp1->getNonzeroElements();
  TEST_ASSERT(nz1.size()>0);

  fp2 = AtomPairs::getTopologicalTorsionFingerprint(*mol,4,&roots);
  SparseIntVect<boost::int64_t>::StorageType nz2=fp2->getNonzeroElements();
  TEST_ASSERT(nz2.size()>0);
  TEST_ASSERT(nz2.size()<nz1.size());

  for(SparseIntVect<boost::int64_t>::StorageType::const_iterator bIt=nz2.begin();
      bIt!=nz2.end();++bIt){
    TEST_ASSERT(bIt->second<=fp2->getVal(bIt->first));
  }

  delete mol;
  delete fp1;
  delete fp2;
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testIgnoreTorsions(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test ignoring atoms in Topological Torsions." << std::endl;

  {
    ROMol *mol;
    SparseIntVect<boost::int64_t> *fp1,*fp2;
    std::vector<boost::uint32_t> roots;


    mol = SmilesToMol("OCCCC");
    roots.push_back(0);

    fp1 = AtomPairs::getTopologicalTorsionFingerprint(*mol);
    SparseIntVect<boost::int64_t>::StorageType nz1=fp1->getNonzeroElements();
    TEST_ASSERT(nz1.size()==2);

    fp2 = AtomPairs::getTopologicalTorsionFingerprint(*mol,4,0,&roots);
    SparseIntVect<boost::int64_t>::StorageType nz2=fp2->getNonzeroElements();
    TEST_ASSERT(nz2.size()==1);

    for(SparseIntVect<boost::int64_t>::StorageType::const_iterator bIt=nz2.begin();
        bIt!=nz2.end();++bIt){
      TEST_ASSERT(bIt->second<=fp2->getVal(bIt->first));
    }

    delete mol;
    delete fp1;
    delete fp2;
  }
  {
    ROMol *mol;
    SparseIntVect<boost::int64_t> *fp2;
    std::vector<boost::uint32_t> roots;

    mol = SmilesToMol("OCCCC");
    roots.push_back(1);

    fp2 = AtomPairs::getTopologicalTorsionFingerprint(*mol,4,0,&roots);
    SparseIntVect<boost::int64_t>::StorageType nz2=fp2->getNonzeroElements();
    TEST_ASSERT(nz2.size()==0);

    delete mol;
    delete fp2;
  }

  {
    ROMol *mol;
    SparseIntVect<boost::int64_t> *fp2;
    std::vector<boost::uint32_t> roots;

    mol = SmilesToMol("OCCCC");
    roots.push_back(0);

    fp2 = AtomPairs::getTopologicalTorsionFingerprint(*mol,4,&roots,&roots);
    SparseIntVect<boost::int64_t>::StorageType nz2=fp2->getNonzeroElements();
    TEST_ASSERT(nz2.size()==0);

    delete mol;
    delete fp2;
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}


void testMorganAtomInfo(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test atom info from morgan fingerprints." << std::endl;

  {
    ROMol *mol;
    SparseIntVect<boost::uint32_t> *fp;
    MorganFingerprints::BitInfoMap bitInfo;
    SparseIntVect<boost::uint32_t>::StorageType nze;

    mol = SmilesToMol("CCCCC");
    fp = MorganFingerprints::getFingerprint(*mol,0,0,0,false,true,true,false,&bitInfo);
    nze=fp->getNonzeroElements();
    TEST_ASSERT(nze.size()==2);
    TEST_ASSERT(bitInfo.size()==2);
    for(SparseIntVect<boost::uint32_t>::StorageType::const_iterator iter=nze.begin();
        iter!=nze.end();++iter){
      TEST_ASSERT(iter->second==bitInfo[iter->first].size());
    }
    for(MorganFingerprints::BitInfoMap::const_iterator iter=bitInfo.begin();
        iter!=bitInfo.end();++iter){
      TEST_ASSERT(iter->second.begin()->second==0);
    }

    delete fp;

    bitInfo.clear();
    fp = MorganFingerprints::getFingerprint(*mol,1,0,0,false,true,true,false,&bitInfo);
    TEST_ASSERT(fp->getNonzeroElements().size()==5);
    for(SparseIntVect<boost::uint32_t>::StorageType::const_iterator iter=nze.begin();
        iter!=nze.end();++iter){
      TEST_ASSERT(iter->second==bitInfo[iter->first].size());
    }
    for(MorganFingerprints::BitInfoMap::const_iterator iter=bitInfo.begin();
        iter!=bitInfo.end();++iter){
      TEST_ASSERT(iter->second.begin()->second==0 ||
                  iter->second.begin()->second==1 );
    }
    delete fp;

    delete mol;
  }

  {
    ROMol *mol;
    ExplicitBitVect *fp;
    MorganFingerprints::BitInfoMap bitInfo;

    mol = SmilesToMol("CCCCC");
    fp = MorganFingerprints::getFingerprintAsBitVect(*mol,0,2048,0,0,false,true,false,&bitInfo);
    TEST_ASSERT(fp->getNumOnBits()==2);
    TEST_ASSERT(bitInfo.size()==2);
    for(MorganFingerprints::BitInfoMap::const_iterator iter=bitInfo.begin();
        iter!=bitInfo.end();++iter){
      TEST_ASSERT(iter->first<2048);
      TEST_ASSERT(fp->getBit(iter->first));
    }
    for(MorganFingerprints::BitInfoMap::const_iterator iter=bitInfo.begin();
        iter!=bitInfo.end();++iter){
      TEST_ASSERT(iter->second.begin()->second==0);
    }

    delete fp;
    bitInfo.clear();
    fp = MorganFingerprints::getFingerprintAsBitVect(*mol,1,2048,0,0,false,true,false,&bitInfo);
    TEST_ASSERT(fp->getNumOnBits()==5);
    TEST_ASSERT(bitInfo.size()==5);
    for(MorganFingerprints::BitInfoMap::const_iterator iter=bitInfo.begin();
        iter!=bitInfo.end();++iter){
      TEST_ASSERT(iter->first<2048);
      TEST_ASSERT(fp->getBit(iter->first));
    }
    for(MorganFingerprints::BitInfoMap::const_iterator iter=bitInfo.begin();
        iter!=bitInfo.end();++iter){
      TEST_ASSERT(iter->second.begin()->second==0 ||
                  iter->second.begin()->second==1 );
    }
    delete fp;
  
    delete mol;
  }

  { // this was github issue #295

    ROMol *mol;
    MorganFingerprints::BitInfoMap bitInfo1,bitInfo2;

    mol = SmilesToMol("CCCCC");

    ExplicitBitVect *fp;
    fp = MorganFingerprints::getFingerprintAsBitVect(*mol,2,2048,0,0,false,true,false,&bitInfo1);
    delete fp;

    SparseIntVect<boost::uint32_t> *iv;
    iv = MorganFingerprints::getHashedFingerprint(*mol,2,2048,0,0,false,true,false,&bitInfo2);
    delete iv;

    TEST_ASSERT(bitInfo1.size()==bitInfo2.size());
    
    for(MorganFingerprints::BitInfoMap::const_iterator iter1=bitInfo1.begin();
        iter1!=bitInfo1.end();++iter1){
      TEST_ASSERT(iter1->first<2048);
      TEST_ASSERT(bitInfo2.find(iter1->first)!=bitInfo2.end());
    }
    
    delete mol;
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}


void testRDKitFPOptions(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdInfoLog) <<"testing RDKit fingerprint options" << std::endl;
  {
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1);
    ExplicitBitVect *fp2=RDKFingerprintMol(*m2);
    TEST_ASSERT(*fp1!=*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  {
    UINT_VECT invars(6,1);
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,7,2048,2,true,0,128,true,true,&invars);
    ExplicitBitVect *fp2=RDKFingerprintMol(*m2,1,7,2048,2,true,0,128,true,true,&invars);
    TEST_ASSERT(*fp1==*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  {
    UINT_VECT invars(6,1);
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1CCCCN1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,7,2048,2,true,0,128,true,false,&invars);
    ExplicitBitVect *fp2=RDKFingerprintMol(*m2,1,7,2048,2,true,0,128,true,false,&invars);
    TEST_ASSERT(*fp1==*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  BOOST_LOG(rdInfoLog) <<"done" << std::endl;
}


void testPairsAndTorsionsOptions(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdInfoLog) <<"testing atom pair and torsions options" << std::endl;
  {
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    SparseIntVect<boost::int32_t> *fp1=AtomPairs::getAtomPairFingerprint(*m1);
    SparseIntVect<boost::int32_t> *fp2=AtomPairs::getAtomPairFingerprint(*m2);
    TEST_ASSERT(*fp1!=*fp2);
    delete fp1;
    delete fp2;

    UINT_VECT invars(6,1);
    fp1=AtomPairs::getAtomPairFingerprint(*m1,
                                          (const std::vector<boost::uint32_t> *)0,
                                          (const std::vector<boost::uint32_t> *)0,
                                          &invars);
    fp2=AtomPairs::getAtomPairFingerprint(*m1,
                                          (const std::vector<boost::uint32_t> *)0,
                                          (const std::vector<boost::uint32_t> *)0,
                                          &invars);

    TEST_ASSERT(*fp1==*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  {
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    SparseIntVect<boost::int32_t> *fp1=AtomPairs::getHashedAtomPairFingerprint(*m1,1024,1,5);
    SparseIntVect<boost::int32_t> *fp2=AtomPairs::getHashedAtomPairFingerprint(*m2,1024,1,5);
    TEST_ASSERT(*fp1!=*fp2);
    delete fp1;
    delete fp2;

    UINT_VECT invars(6,1);
    fp1=AtomPairs::getHashedAtomPairFingerprint(*m1,1024,1,5,
                                          (const std::vector<boost::uint32_t> *)0,
                                          (const std::vector<boost::uint32_t> *)0,
                                          &invars);
    fp2=AtomPairs::getHashedAtomPairFingerprint(*m2,1024,1,5,
                                                (const std::vector<boost::uint32_t> *)0,
                                                (const std::vector<boost::uint32_t> *)0,
                                                &invars);

    TEST_ASSERT(*fp1==*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  {
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    ExplicitBitVect *fp1=AtomPairs::getHashedAtomPairFingerprintAsBitVect(*m1,1024,1,5);
    ExplicitBitVect *fp2=AtomPairs::getHashedAtomPairFingerprintAsBitVect(*m2,1024,1,5);
    TEST_ASSERT(*fp1!=*fp2);
    delete fp1;
    delete fp2;

    UINT_VECT invars(6,1);
    fp1=AtomPairs::getHashedAtomPairFingerprintAsBitVect(*m1,1024,1,5,
                                                         (const std::vector<boost::uint32_t> *)0,
                                                         (const std::vector<boost::uint32_t> *)0,
                                                         &invars);
    fp2=AtomPairs::getHashedAtomPairFingerprintAsBitVect(*m2,1024,1,5,
                                                         (const std::vector<boost::uint32_t> *)0,
                                                         (const std::vector<boost::uint32_t> *)0,
                                                         &invars);

    TEST_ASSERT(*fp1==*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  {
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    SparseIntVect<boost::int64_t> *fp1=AtomPairs::getTopologicalTorsionFingerprint(*m1);
    SparseIntVect<boost::int64_t> *fp2=AtomPairs::getTopologicalTorsionFingerprint(*m2);
    TEST_ASSERT(*fp1!=*fp2);
    delete fp1;
    delete fp2;

    UINT_VECT invars(6,1);
    fp1=AtomPairs::getTopologicalTorsionFingerprint(*m1,4,
                                                    (const std::vector<boost::uint32_t> *)0,
                                                    (const std::vector<boost::uint32_t> *)0,
                                                    &invars);
    fp2=AtomPairs::getTopologicalTorsionFingerprint(*m2,4,
                                                    (const std::vector<boost::uint32_t> *)0,
                                                    (const std::vector<boost::uint32_t> *)0,
                                                    &invars);

    TEST_ASSERT(*fp1==*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  {
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    SparseIntVect<boost::int64_t> *fp1=AtomPairs::getHashedTopologicalTorsionFingerprint(*m1);
    SparseIntVect<boost::int64_t> *fp2=AtomPairs::getHashedTopologicalTorsionFingerprint(*m2);

    TEST_ASSERT(*fp1!=*fp2);
    delete fp1;
    delete fp2;

    UINT_VECT invars(6,1);
    fp1=AtomPairs::getHashedTopologicalTorsionFingerprint(*m1,1024,4,
                                                          (const std::vector<boost::uint32_t> *)0,
                                                          (const std::vector<boost::uint32_t> *)0,
                                                          &invars);
    fp2=AtomPairs::getHashedTopologicalTorsionFingerprint(*m2,1024,4,
                                                          (const std::vector<boost::uint32_t> *)0,
                                                          (const std::vector<boost::uint32_t> *)0,
                                                          &invars);
    TEST_ASSERT(*fp1==*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  {
    std::string smi = "C1=CC=CC=C1";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    smi = "C1=CC=CC=N1";
    RWMol *m2 = SmilesToMol(smi);
    TEST_ASSERT(m2);
    ExplicitBitVect *fp1=AtomPairs::getHashedTopologicalTorsionFingerprintAsBitVect(*m1);
    ExplicitBitVect *fp2=AtomPairs::getHashedTopologicalTorsionFingerprintAsBitVect(*m2);

    TEST_ASSERT(*fp1!=*fp2);
    delete fp1;
    delete fp2;

    UINT_VECT invars(6,1);
    fp1=AtomPairs::getHashedTopologicalTorsionFingerprintAsBitVect(*m1,1024,4,
                                                          (const std::vector<boost::uint32_t> *)0,
                                                          (const std::vector<boost::uint32_t> *)0,
                                                          &invars);
    fp2=AtomPairs::getHashedTopologicalTorsionFingerprintAsBitVect(*m2,1024,4,
                                                          (const std::vector<boost::uint32_t> *)0,
                                                          (const std::vector<boost::uint32_t> *)0,
                                                          &invars);
    TEST_ASSERT(*fp1==*fp2);
    delete m1;
    delete m2;
    delete fp1;
    delete fp2;
  }
  
  BOOST_LOG(rdInfoLog) <<"done" << std::endl;
}

void testRDKitFromAtoms(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdInfoLog) <<"testing RDKit fingerprints rooted at particular atoms" << std::endl;
  {
    std::string smi = "CCCCCC";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    std::vector<boost::uint32_t> fromAtoms;
    fromAtoms.push_back(0);
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,4,2048,1,true,0,128,true,true,0,&fromAtoms);
    TEST_ASSERT(fp1->getNumOnBits()==4);
    delete m1;
    delete fp1;
  }
  {
    std::string smi = "CCCCCO";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    std::vector<boost::uint32_t> fromAtoms;
    fromAtoms.push_back(0);
    fromAtoms.push_back(5);
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,4,2048,1,true,0,128,true,true,0,&fromAtoms);
    TEST_ASSERT(fp1->getNumOnBits()==8);
    delete m1;
    delete fp1;
  }
  {
    std::string smi = "CCCCCO";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    std::vector<boost::uint32_t> fromAtoms;
    fromAtoms.push_back(0);
    fromAtoms.push_back(5);
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,4,2048,1,true,0,128,false,true,0,&fromAtoms);
    TEST_ASSERT(fp1->getNumOnBits()==8);
    delete m1;
    delete fp1;
  }
  {
    std::string smi = "CCCCCO";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    std::vector<boost::uint32_t> fromAtoms;
    fromAtoms.push_back(0);
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0xFFFFFFFF,1,4,2048,0,0,true,&fromAtoms);
    TEST_ASSERT(fp1->getNumOnBits()==20);
    delete m1;
    delete fp1;
  }
  {
    std::string smi = "CCCCCO";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    std::vector<boost::uint32_t> fromAtoms;
    fromAtoms.push_back(0);
    fromAtoms.push_back(5);
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0xFFFFFFFF,1,4,2048,0,0,true,&fromAtoms);
    TEST_ASSERT(fp1->getNumOnBits()==24);
    delete m1;
    delete fp1;
  }
  {
    std::string smi = "CCCCCO";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    std::vector<boost::uint32_t> fromAtoms;
    fromAtoms.push_back(0);
    fromAtoms.push_back(5);
    ExplicitBitVect *fp1=LayeredFingerprintMol(*m1,0xFFFFFFFF,1,4,2048,0,0,false,&fromAtoms);
    TEST_ASSERT(fp1->getNumOnBits()==24);
    delete m1;
    delete fp1;
  }
  BOOST_LOG(rdInfoLog) <<"done" << std::endl;
}

void testMACCS(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdInfoLog) <<"testing MACCS key calculation" << std::endl;
  {
    std::string smi = "CNO";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    ExplicitBitVect *fp1=MACCSFingerprints::getFingerprintAsBitVect(*m1);
    TEST_ASSERT(fp1->getNumOnBits()==15);
    unsigned int _onBits[]={24, 68, 69, 71, 93, 94, 102, 124, 131, 139, 151, 158, 160, 161, 164};
    std::vector<unsigned int> onBits(_onBits,_onBits+sizeof(_onBits)/sizeof(*_onBits));
    BOOST_FOREACH(unsigned int ob,onBits){
      TEST_ASSERT((*fp1)[ob]);
    }
    delete m1;
    delete fp1;
  }
  {
    std::string smi = "CCC";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    ExplicitBitVect *fp1=MACCSFingerprints::getFingerprintAsBitVect(*m1);
    TEST_ASSERT(fp1->getNumOnBits()==5);
    unsigned int _onBits[]={74, 114, 149, 155, 160};
    std::vector<unsigned int> onBits(_onBits,_onBits+sizeof(_onBits)/sizeof(*_onBits));
    BOOST_FOREACH(unsigned int ob,onBits){
      TEST_ASSERT((*fp1)[ob]);
    }
    delete m1;
    delete fp1;
  }
  {
    std::string smi = "CC.CO";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    ExplicitBitVect *fp1=MACCSFingerprints::getFingerprintAsBitVect(*m1);
    TEST_ASSERT(fp1->getNumOnBits()==8);
    unsigned int _onBits[]={93, 139, 141, 149, 157, 160, 164, 166};
    std::vector<unsigned int> onBits(_onBits,_onBits+sizeof(_onBits)/sizeof(*_onBits));
    BOOST_FOREACH(unsigned int ob,onBits){
      TEST_ASSERT((*fp1)[ob]);
    }
    delete m1;
    delete fp1;
  }
  {
    // check that bit 44 "OTHER" gets properly set:
    std::string smi = "CC[SeH]";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    ExplicitBitVect *fp1=MACCSFingerprints::getFingerprintAsBitVect(*m1);
    TEST_ASSERT((*fp1)[44]);
    delete m1;
    delete fp1;
  }
  BOOST_LOG(rdInfoLog) <<"done" << std::endl;
}


void testRDKitAtomBits(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdInfoLog) <<"testing RDKit fingerprints reporting atomBits" << std::endl;
  {
    std::string smi = "CCCCCC";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    std::vector<std::vector<boost::uint32_t> > atomBits(m1->getNumAtoms());
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,4,2048,1,true,0,128,true,true,0,0,&atomBits);
    TEST_ASSERT(fp1->getNumOnBits()==4);
    for(unsigned int i=0;i<m1->getNumAtoms();++i){
      TEST_ASSERT(atomBits[i].size()==4);
    }
    delete m1;
    delete fp1;
  }
  {
    std::string smi = "CCCO";
    RWMol *m1 = SmilesToMol(smi);
    TEST_ASSERT(m1);
    std::vector<std::vector<boost::uint32_t> > atomBits(m1->getNumAtoms());
    ExplicitBitVect *fp1=RDKFingerprintMol(*m1,1,2,2048,1,true,0,128,true,true,0,0,&atomBits);
    TEST_ASSERT(fp1->getNumOnBits()==4);
    TEST_ASSERT(atomBits[0].size()==2);
    TEST_ASSERT(atomBits[1].size()==3);
    TEST_ASSERT(atomBits[2].size()==4);
    TEST_ASSERT(atomBits[3].size()==2);
    delete m1;
    delete fp1;
  }
  BOOST_LOG(rdInfoLog) <<"done" << std::endl;
}


void testChiralPairs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Atom Pairs including info about chirality." << std::endl;

  ROMol *m1,*m2,*m3;

  m1 = SmilesToMol("CC[CH](F)Cl");
  TEST_ASSERT(m1);
  m2 = SmilesToMol("CC[C@H](F)Cl");
  TEST_ASSERT(m1);
  m3 = SmilesToMol("CC[C@@H](F)Cl");
  TEST_ASSERT(m1);

  {
    SparseIntVect<int> *fp1,*fp2,*fp3;
    fp1 = AtomPairs::getAtomPairFingerprint(*m1,1,5);
    TEST_ASSERT(fp1->getTotalVal()==10);
    TEST_ASSERT(fp1->getNonzeroElements().size()==10);
    fp2 = AtomPairs::getAtomPairFingerprint(*m2,1,5);
    TEST_ASSERT(fp2->getTotalVal()==10);
    TEST_ASSERT(fp2->getNonzeroElements().size()==10);
    fp3 = AtomPairs::getAtomPairFingerprint(*m3,1,5);
    TEST_ASSERT(fp3->getTotalVal()==10);
    TEST_ASSERT(fp3->getNonzeroElements().size()==10);

    TEST_ASSERT((*fp1)==(*fp2));
    TEST_ASSERT((*fp1)==(*fp3));
    TEST_ASSERT((*fp2)==(*fp3));
  
    delete fp1;
    delete fp2;
    delete fp3;
  
    fp1 = AtomPairs::getAtomPairFingerprint(*m1,1,5,0,0,0,true);
    TEST_ASSERT(fp1->getTotalVal()==10);
    TEST_ASSERT(fp1->getNonzeroElements().size()==10);
    fp2 = AtomPairs::getAtomPairFingerprint(*m2,1,5,0,0,0,true);
    TEST_ASSERT(fp2->getTotalVal()==10);
    TEST_ASSERT(fp2->getNonzeroElements().size()==10);
    fp3 = AtomPairs::getAtomPairFingerprint(*m3,1,5,0,0,0,true);
    TEST_ASSERT(fp3->getTotalVal()==10);
    TEST_ASSERT(fp3->getNonzeroElements().size()==10);

    TEST_ASSERT((*fp1)!=(*fp2));
    TEST_ASSERT((*fp1)!=(*fp3));
    TEST_ASSERT((*fp2)!=(*fp3));
  
    delete fp1;
    delete fp2;
    delete fp3;
  }
  
  {
    SparseIntVect<int> *fp1,*fp2,*fp3;
    fp1 = AtomPairs::getHashedAtomPairFingerprint(*m1,4096,1,5);
    TEST_ASSERT(fp1->getTotalVal()==10);
    TEST_ASSERT(fp1->getNonzeroElements().size()==10);
    fp2 = AtomPairs::getHashedAtomPairFingerprint(*m2,4096,1,5);
    TEST_ASSERT(fp2->getTotalVal()==10);
    TEST_ASSERT(fp2->getNonzeroElements().size()==10);
    fp3 = AtomPairs::getHashedAtomPairFingerprint(*m3,4096,1,5);
    TEST_ASSERT(fp3->getTotalVal()==10);
    TEST_ASSERT(fp3->getNonzeroElements().size()==10);

    TEST_ASSERT((*fp1)==(*fp2));
    TEST_ASSERT((*fp1)==(*fp3));
    TEST_ASSERT((*fp2)==(*fp3));
  
    delete fp1;
    delete fp2;
    delete fp3;
  
    fp1 = AtomPairs::getHashedAtomPairFingerprint(*m1,4096,1,5,0,0,0,true);
    TEST_ASSERT(fp1->getTotalVal()==10);
    TEST_ASSERT(fp1->getNonzeroElements().size()==10);
    fp2 = AtomPairs::getHashedAtomPairFingerprint(*m2,4096,1,5,0,0,0,true);
    TEST_ASSERT(fp2->getTotalVal()==10);
    TEST_ASSERT(fp2->getNonzeroElements().size()==10);
    fp3 = AtomPairs::getHashedAtomPairFingerprint(*m3,4096,1,5,0,0,0,true);
    TEST_ASSERT(fp3->getTotalVal()==10);
    TEST_ASSERT(fp3->getNonzeroElements().size()==10);

    TEST_ASSERT((*fp1)!=(*fp2));
    TEST_ASSERT((*fp1)!=(*fp3));
    TEST_ASSERT((*fp2)!=(*fp3));
  
    delete fp1;
    delete fp2;
    delete fp3;
  }
  

  delete m1;
  delete m2;
  delete m3;
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}
void testChiralTorsions(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test Topological Torsions including info about chirality." << std::endl;

  ROMol *m1,*m2,*m3;

  m1 = SmilesToMol("CC[CH](F)Cl");
  TEST_ASSERT(m1);
  m2 = SmilesToMol("CC[C@H](F)Cl");
  TEST_ASSERT(m1);
  m3 = SmilesToMol("CC[C@@H](F)Cl");
  TEST_ASSERT(m1);

  {
    SparseIntVect<boost::int64_t> *fp1,*fp2,*fp3;
    fp1 = AtomPairs::getTopologicalTorsionFingerprint(*m1);
    TEST_ASSERT(fp1->getTotalVal()==2);
    TEST_ASSERT(fp1->getNonzeroElements().size()==2);
    fp2 = AtomPairs::getTopologicalTorsionFingerprint(*m2);
    TEST_ASSERT(fp2->getTotalVal()==2);
    TEST_ASSERT(fp2->getNonzeroElements().size()==2);
    fp3 = AtomPairs::getTopologicalTorsionFingerprint(*m3);
    TEST_ASSERT(fp3->getTotalVal()==2);
    TEST_ASSERT(fp3->getNonzeroElements().size()==2);

    TEST_ASSERT((*fp1)==(*fp2));
    TEST_ASSERT((*fp1)==(*fp3));
    TEST_ASSERT((*fp2)==(*fp3));
  
    delete fp1;
    delete fp2;
    delete fp3;
  
    fp1 = AtomPairs::getTopologicalTorsionFingerprint(*m1,4,0,0,0,true);
    TEST_ASSERT(fp1->getTotalVal()==2);
    TEST_ASSERT(fp1->getNonzeroElements().size()==2);
    fp2 = AtomPairs::getTopologicalTorsionFingerprint(*m2,4,0,0,0,true);
    TEST_ASSERT(fp2->getTotalVal()==2);
    TEST_ASSERT(fp2->getNonzeroElements().size()==2);
    fp3 = AtomPairs::getTopologicalTorsionFingerprint(*m3,4,0,0,0,true);
    TEST_ASSERT(fp3->getTotalVal()==2);
    TEST_ASSERT(fp3->getNonzeroElements().size()==2);

    TEST_ASSERT((*fp1)!=(*fp2));
    TEST_ASSERT((*fp1)!=(*fp3));
    TEST_ASSERT((*fp2)!=(*fp3));
  
    delete fp1;
    delete fp2;
    delete fp3;
  }
  
  {
    SparseIntVect<boost::int64_t> *fp1,*fp2,*fp3;
    fp1 = AtomPairs::getHashedTopologicalTorsionFingerprint(*m1,4096);
    TEST_ASSERT(fp1->getTotalVal()==2);
    TEST_ASSERT(fp1->getNonzeroElements().size()==2);
    fp2 = AtomPairs::getHashedTopologicalTorsionFingerprint(*m2,4096);
    TEST_ASSERT(fp2->getTotalVal()==2);
    TEST_ASSERT(fp2->getNonzeroElements().size()==2);
    fp3 = AtomPairs::getHashedTopologicalTorsionFingerprint(*m3,4096);
    TEST_ASSERT(fp3->getTotalVal()==2);
    TEST_ASSERT(fp3->getNonzeroElements().size()==2);

    TEST_ASSERT((*fp1)==(*fp2));
    TEST_ASSERT((*fp1)==(*fp3));
    TEST_ASSERT((*fp2)==(*fp3));
  
    delete fp1;
    delete fp2;
    delete fp3;
  
    fp1 = AtomPairs::getHashedTopologicalTorsionFingerprint(*m1,4096,4,0,0,0,true);
    TEST_ASSERT(fp1->getTotalVal()==2);
    TEST_ASSERT(fp1->getNonzeroElements().size()==2);
    fp2 = AtomPairs::getHashedTopologicalTorsionFingerprint(*m2,4096,4,0,0,0,true);
    TEST_ASSERT(fp2->getTotalVal()==2);
    TEST_ASSERT(fp2->getNonzeroElements().size()==2);
    fp3 = AtomPairs::getHashedTopologicalTorsionFingerprint(*m3,4096,4,0,0,0,true);
    TEST_ASSERT(fp3->getTotalVal()==2);
    TEST_ASSERT(fp3->getNonzeroElements().size()==2);

    TEST_ASSERT((*fp1)!=(*fp2));
    TEST_ASSERT((*fp1)!=(*fp3));
    TEST_ASSERT((*fp2)!=(*fp3));
  
    delete fp1;
    delete fp2;
    delete fp3;
  }
  

  delete m1;
  delete m2;
  delete m3;
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testGitHubIssue25(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test GitHub Issue 25: fingerprint backwards compatibility." << std::endl;

  {
    ROMol *m1 = SmilesToMol("CCCCO");
    TEST_ASSERT(m1);
    SparseIntVect<boost::int64_t> *fp1;
    fp1 = AtomPairs::getTopologicalTorsionFingerprint(*m1);
    TEST_ASSERT(fp1);
    TEST_ASSERT(fp1->getTotalVal()==2);
    TEST_ASSERT(fp1->getNonzeroElements().size()==2);
    TEST_ASSERT((*fp1)[4437590048LL]==1);
    TEST_ASSERT((*fp1)[12893306913LL]==1);
    delete fp1;
    delete m1;
  }
  {
    ROMol *m1 = SmilesToMol("CCCCO");
    TEST_ASSERT(m1);
    SparseIntVect<boost::int64_t> *fp1;
    fp1 = AtomPairs::getHashedTopologicalTorsionFingerprint(*m1,1000);
    TEST_ASSERT(fp1);
    TEST_ASSERT(fp1->getTotalVal()==2);
    TEST_ASSERT(fp1->getNonzeroElements().size()==2);
    TEST_ASSERT((*fp1)[24]==1);
    TEST_ASSERT((*fp1)[288]==1);
    delete fp1;
    delete m1;
  }
  {
    ROMol *m1 = SmilesToMol("CCO");
    TEST_ASSERT(m1);
    SparseIntVect<boost::int32_t> *fp1;
    fp1 = AtomPairs::getAtomPairFingerprint(*m1);
    TEST_ASSERT(fp1);
    TEST_ASSERT(fp1->getTotalVal()==3);
    TEST_ASSERT(fp1->getNonzeroElements().size()==3);
    TEST_ASSERT((*fp1)[558113]==1);
    TEST_ASSERT((*fp1)[1590306]==1);
    TEST_ASSERT((*fp1)[1590337]==1);
    delete fp1;
    delete m1;
  }
  {
    ROMol *m1 = SmilesToMol("CCO");
    TEST_ASSERT(m1);
    SparseIntVect<boost::int32_t> *fp1;
    fp1 = AtomPairs::getHashedAtomPairFingerprint(*m1);
    TEST_ASSERT(fp1);
    TEST_ASSERT(fp1->getTotalVal()==3);
    TEST_ASSERT(fp1->getNonzeroElements().size()==3);
    TEST_ASSERT((*fp1)[1375]==1);
    TEST_ASSERT((*fp1)[1423]==1);
    TEST_ASSERT((*fp1)[1503]==1);
    delete fp1;
    delete m1;
  }


  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testGitHubIssue151(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test GitHub Issue 151: PatternFingerprint problems" << std::endl;


  {
    ROMol *qm = SmilesToMol("CCCn1c2ccccc2c2ccccc21");
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("O=C1NCc2c1c1c3cc(Br)ccc3n3c1c1c2c2ccccc2n1CC(CO)C3");
    TEST_ASSERT(m);
    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);
    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));

    delete qm;
    delete m;
  }
  {
    ROMol *qm = SmilesToMol("c1ccc2c(c1)[nH]c1ccccc12");
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("O=C1NCc2c1c1c3cc(Br)ccc3n3c1c1c2c2ccccc2n1CC(CO)C3");
    TEST_ASSERT(m);
    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);
    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));

    delete qm;
    delete m;
  }
  {
    ROMol *qm = SmilesToMol("CC(C)c1nnc(N)[nH]1");
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("CC(C)c1nc2NCCCn2n1");
    TEST_ASSERT(m);
    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);
    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));

    delete qm;
    delete m;
  }
  {
    ROMol *qm = SmilesToMol("CC(C)c1nnc(N)[nH]1");
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("CN1c2nc(C3CCN(S(=O)(=O)c4ccc(Cl)cc4Cl)CC3)nn2S(=O)(=O)c2ccccc21");
    TEST_ASSERT(m);
    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);
    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));

    delete qm;
    delete m;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}


void test3DAtomPairs(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test 3D atom pairs." << std::endl;

  std::string fName= getenv("RDBASE");
  fName += "/Code/GraphMol/Fingerprints/testData/triangle.sdf";
  SDMolSupplier suppl(fName);
  {
    ROMol *mol=suppl.next();
    SparseIntVect<boost::int32_t> *fp;
    // do the 3D version
    fp = AtomPairs::getHashedAtomPairFingerprint(*mol,2048,1,AtomPairs::maxPathLen-1,0,0,0,false,false);
    TEST_ASSERT(fp->getTotalVal()==3);
    TEST_ASSERT(fp->getNonzeroElements().size()==1);
    delete fp;
    // now do the 2D version
    fp = AtomPairs::getHashedAtomPairFingerprint(*mol,2048,1,AtomPairs::maxPathLen-1,0,0,0,false,true);
    TEST_ASSERT(fp->getTotalVal()==3);
    TEST_ASSERT(fp->getNonzeroElements().size()==1);
    delete fp;

    // we should get a conformer exception if there are no conformers:
    mol->clearConformers();
    bool ok=false;
    try{
      fp = AtomPairs::getHashedAtomPairFingerprint(*mol,2048,1,AtomPairs::maxPathLen-1,0,0,0,false,false);
    } catch (ConformerException &e){
      ok=true;
    }
    TEST_ASSERT(ok);
    
    delete mol;
  }
  {
    ROMol *mol=suppl.next();
    SparseIntVect<boost::int32_t> *fp;
    // do the 3D version
    fp = AtomPairs::getHashedAtomPairFingerprint(*mol,2048,1,AtomPairs::maxPathLen-1,0,0,0,false,false);
    TEST_ASSERT(fp->getTotalVal()==3);
    TEST_ASSERT(fp->getNonzeroElements().size()==2);
    delete fp;
    // now do the 2D version
    fp = AtomPairs::getHashedAtomPairFingerprint(*mol,2048,1,AtomPairs::maxPathLen-1,0,0,0,false,true);
    TEST_ASSERT(fp->getTotalVal()==3);
    TEST_ASSERT(fp->getNonzeroElements().size()==1);
    delete fp;
    delete mol;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testGitHubIssue195(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule" << std::endl;

  {
    ROMol *m1=new ROMol();
    ExplicitBitVect *fp1=MACCSFingerprints::getFingerprintAsBitVect(*m1);
    TEST_ASSERT(fp1->getNumOnBits()==0);

    delete m1;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testGitHubIssue258(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test GitHub Issue 258: Bad pattern fingerprint for query molecule" << std::endl;

  {
    ROMol *qm = SmartsToMol("n2c(-[#6])ccc2-[#6]",
                            0,true);
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("Clc1c(cccc1)-n2c(c(cc2C)C=NNC(=O)CSc3ncccn3)C");
    TEST_ASSERT(m);

    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);
    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));

    delete qm;
    delete m;
    delete qbv;
    delete mbv;
  }
  {
    ROMol *qm = SmartsToMol("n2c(cc(c2-[#6]))-[#6]",
                            0,true);
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("Clc1c(cccc1)-n2c(c(cc2C)C=NNC(=O)CSc3ncccn3)C");
    TEST_ASSERT(m);

    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);
    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));

    delete qm;
    delete m;
    delete qbv;
    delete mbv;
  }
  {
    ROMol *qm = SmartsToMol("n2(-[#6]:1:[!#1]:[#6]:[#6]:[#6]:[#6]:1)c(cc(c2-[#6;X4]))-[#6;X4]",
                            0,true);
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("n2(-c:1:c:c:c:c:c:1)c(cc(c2-C))-C",
                            0,true);
    TEST_ASSERT(m);

    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);

#if 0
    ExplicitBitVect dv=(*qbv)^((*qbv)&(*mbv));
    IntVect iv;
    dv.getOnBits(iv);
    std::cerr<<"\n\n";
    std::copy(iv.begin(),iv.end(),std::ostream_iterator<int>(std::cerr,", "));
    std::cerr<<std::endl;
#endif
    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));


    
    delete qm;
    delete m;
    delete qbv;
    delete mbv;
  }
  {
    ROMol *qm = SmartsToMol("n2(-[#6]:1:[!#1]:[#6]:[#6]:[#6]:[#6]:1)c(cc(c2-[#6;X4]))-[#6;X4]",
                            0,true);
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("Clc1c(cccc1)-n2c(c(cc2C)C=NNC(=O)CSc3ncccn3)C");
    TEST_ASSERT(m);

    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);

    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));
    
    delete qm;
    delete m;
    delete qbv;
    delete mbv;
  }
  {
    ROMol *qm = SmartsToMol("n2(-[#6]:1:[!#1]:[#6]:[#6]:[#6]:[#6]:1)c(cc(c2-[#6;X4])-[#1])-[#6;X4]",
                            0,true);
    TEST_ASSERT(qm);
    ROMol *m = SmilesToMol("Clc1c(cccc1)-n2c(c(cc2C)C=NNC(=O)CSc3ncccn3)C");
    TEST_ASSERT(m);

    ExplicitBitVect *qbv=PatternFingerprintMol(*qm,2048);
    ExplicitBitVect *mbv=PatternFingerprintMol(*m,2048);
    MatchVectType mv;
    TEST_ASSERT(SubstructMatch(*m,*qm,mv));
    TEST_ASSERT(AllProbeBitsMatch(*qbv,*mbv));

    delete qm;
    delete m;
    delete qbv;
    delete mbv;
  }

  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}



#ifdef RDK_TEST_MULTITHREADED
namespace {
  void runblock(const std::vector<ROMol *> &mols,unsigned int count,unsigned int idx,
                const std::vector<ExplicitBitVect *> &referenceData,
                unsigned int nReps){
    for(unsigned int j=0;j<nReps;j++){
      for(unsigned int i=0;i<mols.size();++i){
        if(i%count != idx) continue;
        ROMol *mol = mols[i];
        ExplicitBitVect *lbv=PatternFingerprintMol(*mol,2048);
        if(referenceData.size() && referenceData[i])
          TEST_ASSERT((*lbv)==(*referenceData[i]));
        delete lbv;
      }
    }
  };
}

#include <boost/thread.hpp>  
void testMultithreadedPatternFP(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test multithreading with the pattern FP" << std::endl;

  std::string fName = getenv("RDBASE");
  fName += "/Data/NCI/first_200.props.sdf";
  SDMolSupplier suppl(fName);
  std::cerr<<"reading molecules"<<std::endl;
  std::vector<ROMol *> mols;
  std::vector<ExplicitBitVect *> referenceData;
  while(!suppl.atEnd()&&mols.size()<100){
    ROMol *mol=0;
    try{
      mol=suppl.next();
    } catch(...){
      continue;
    }
    if(!mol) continue;
    mols.push_back(mol);
  }
  boost::thread_group tg;

  std::cerr<<"pass 1"<<std::endl;
  unsigned int count=4;
  for(unsigned int i=0;i<count;++i){
    std::cerr<<" launch :"<<i<<std::endl;std::cerr.flush();
    tg.add_thread(new boost::thread(runblock,mols,count,i,referenceData,10));
  }
  tg.join_all();

  BOOST_FOREACH(const ROMol *mol,mols){
    ExplicitBitVect *bv=PatternFingerprintMol(*mol,2048);
    referenceData.push_back(bv);
  }
  std::cerr<<"pass 2"<<std::endl;
  for(unsigned int i=0;i<count;++i){
    std::cerr<<" launch :"<<i<<std::endl;std::cerr.flush();
    tg.add_thread(new boost::thread(runblock,mols,count,i,referenceData,300));
  }
  tg.join_all();

  for(unsigned int i=0;i<mols.size();++i){
    delete mols[i];
    delete referenceData[i];
  }


  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}
#else
void testMultithreadedPatternFP(){
}
#endif

void testGitHubIssue334(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP." << std::endl;

  {
    ROMol *m1 = SmilesToMol("N#C");
    TEST_ASSERT(m1);
    SparseIntVect<boost::int32_t> *fp1;
    fp1 = AtomPairs::getAtomPairFingerprint(*m1);
    TEST_ASSERT(fp1);
    delete m1;

    m1 = SmilesToMol("N#[CH]");
    SparseIntVect<boost::int32_t> *fp2;
    fp2 = AtomPairs::getAtomPairFingerprint(*m1);
    TEST_ASSERT(fp2);
    delete m1;

    TEST_ASSERT(fp1->getTotalVal()==fp2->getTotalVal());
    TEST_ASSERT(fp1->getNonzeroElements().size()==fp2->getNonzeroElements().size());
    TEST_ASSERT(*fp1==*fp2);
    delete fp1;
    delete fp2;
  }
  {
    ROMol *m1 = SmilesToMol("N#C");
    TEST_ASSERT(m1);
    SparseIntVect<boost::int64_t> *fp1;
    fp1 = AtomPairs::getTopologicalTorsionFingerprint(*m1);
    TEST_ASSERT(fp1);
    delete m1;

    m1 = SmilesToMol("N#[CH]");
    SparseIntVect<boost::int64_t> *fp2;
    fp2 = AtomPairs::getTopologicalTorsionFingerprint(*m1);
    TEST_ASSERT(fp2);
    delete m1;

    TEST_ASSERT(fp1->getTotalVal()==fp2->getTotalVal());
    TEST_ASSERT(fp1->getNonzeroElements().size()==fp2->getNonzeroElements().size());
    TEST_ASSERT(*fp1==*fp2);
    delete fp1;
    delete fp2;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}


int main(int argc,char *argv[]){
  RDLog::InitLogs();
#if 1
  test1();
  test2();
  test3();
  test1alg2();
  test2alg2();
  test4Trends();
  test1Layers();
  test2Layers();
  test3Layers();
  test1MorganFPs();
  test2MorganFPsFromAtoms();
  test3MorganFPs();
  test4MorganFPs();
  test5MorganFPs();
  //test5BackwardsCompatibility();
  //testIssue2875658();
  testAtomCodes();
  testAtomPairs();
  testAtomPairs2();
  testTorsions();
  testBulkTorsions();
  testHashedAtomPairs();
  testHashedTorsions();
  testRootedAtomPairs();
  testIgnoreAtomPairs();
  testRootedTorsions();
  testIgnoreTorsions();
  testMorganAtomInfo();
  testRDKitFPOptions();
  testPairsAndTorsionsOptions();
  testMACCS();
  testRDKitFromAtoms();
  testRDKitAtomBits();
  testChiralPairs();
  testChiralTorsions();
  testGitHubIssue25();
  testGitHubIssue151();
  test3DAtomPairs();
  testGitHubIssue195();
  testMultithreadedPatternFP();
#endif
  testGitHubIssue258();
  testGitHubIssue334();

  return 0;
}