C++ ForceField::initialize方法代码示例

void testSFIssue2378119() {
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing SFIssue2378119." << std::endl;

  std::string pathName = getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
  {
    RWMol *mol = MolFileToMol(pathName + "/Issue2378119.mol");
    TEST_ASSERT(mol);
    ForceFields::ForceField *field = MMFF::constructForceField(*mol);
    TEST_ASSERT(field);
    field->initialize();
    double e1 = field->calcEnergy();
    TEST_ASSERT(e1 > 0.0 && e1 < 1.0e12);

    int needMore = field->minimize(200, 1.0e-6, 1.0e-3);
    TEST_ASSERT(!needMore);
    double e2 = field->calcEnergy();
    TEST_ASSERT(e2 < e1);

    delete mol;
    delete field;
  }
  {
    RWMol *mol = MolFileToMol(pathName + "/Issue2378119.2.mol");
    TEST_ASSERT(mol);
    ForceFields::ForceField *field = MMFF::constructForceField(*mol);
    TEST_ASSERT(field);
    field->initialize();
    double e1 = field->calcEnergy();
    TEST_ASSERT(e1 == 0.0);

    int needMore = field->minimize(200, 1.0e-6, 1.0e-3);
    TEST_ASSERT(!needMore);
    double e2 = field->calcEnergy();
    TEST_ASSERT(e2 == e1);

    delete mol;
    delete field;
  }
  {
    RWMol *mol = MolFileToMol(pathName + "/Issue2378119.2.mol");
    TEST_ASSERT(mol);
    ForceFields::ForceField *field =
        MMFF::constructForceField(*mol, 100.0, -1, false);
    TEST_ASSERT(field);
    field->initialize();
    double e1 = field->calcEnergy();
    TEST_ASSERT(e1 > 0.0 && e1 < 1.0e12);

    int needMore = field->minimize(200, 1.0e-6, 1.0e-3);
    TEST_ASSERT(!needMore);
    double e2 = field->calcEnergy();
    TEST_ASSERT(e2 < e1);

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

void testIssue239(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing Issue239." << std::endl;

  RWMol *mol;
  int needMore;
  ForceFields::ForceField *field;
  double e1,e2;

  std::string pathName=getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
  mol = MolFileToMol(pathName+"/Issue239.mol",false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);

  field=UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  needMore = field->minimize(200,1e-6,1e-3);
  e1 = field->calcEnergy();
  needMore = field->minimize(200,1e-6,1e-3);
  e2 = field->calcEnergy();
  TEST_ASSERT(feq(e2,e1,0.1));
  
  delete mol;
  delete field;
  

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

void testUFFBuilderSpecialCases(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing UFF special cases." << std::endl;

  RWMol *mol;
  std::string key;
  int needMore;
  RDGeom::Point3D v1,v2;
  ForceFields::ForceField *field;

  std::string pathName=getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
  // ----------
  //  Trigonal bipyramid
  // ----------
  mol = MolFileToMol(pathName+"/tbp.mol",false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);

  const Conformer &conf = mol->getConformer();
  field=UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  needMore = field->minimize(200,1e-8,1e-4);
  TEST_ASSERT(!needMore);
  v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(1));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(2));
  TEST_ASSERT(feq(v1.dotProduct(v2),-1.0,1e-3));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
  TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
  TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
  TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));

  v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(2));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
  TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
  TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
  TEST_ASSERT(feq(v1.dotProduct(v2),0.0,1e-3));

  v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(3));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
  TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
  TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));

  v1 = conf.getAtomPos(0).directionVector(conf.getAtomPos(4));
  v2 = conf.getAtomPos(0).directionVector(conf.getAtomPos(5));
  TEST_ASSERT(feq(v1.dotProduct(v2),-0.5,1e-3));

  
  delete mol;
  delete field;
  

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

void runMol(ROMol *mol,int checkEvery=10,bool verbose=true){
  ForceFields::ForceField *field;

  std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;

  try{
    field=UFF::constructForceField(*mol,2.5);
  } catch (...) {
    field=0;
  }
  if(field){
    field->initialize();
    int needMore=1;
    int nPasses=0;
    while(needMore){
#if 1
      needMore = field->minimize(checkEvery);
      if(verbose) std::cerr << "\t" << ++nPasses << std::endl;
#else
      needMore = field->minimize(1);
      std::cout << MolToMolBlock(mol) << "$$$$" << std::endl;
#endif
    }
    std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;
    delete field;
  } else {
    std::cerr << "failed";
  }
  
}

void testIssue242()
{
// FIX: Changes to the forcefield (connected to Issue 408) have
// made it so that this particular problem no longer manifests
// in this molecule/embedding. A new test case is needed.
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing Issue242." << std::endl;

  RWMol *mol, *mol2;
  int needMore;
  ForceFields::ForceField *field = 0, *field2 = 0;
  std::string mb1,mb2;
  double e1,e2;

  std::string pathName = getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";

  mol = MolFileToMol(pathName + "/Issue242-2.mol");
  TEST_ASSERT(mol);

  mol2 = MolFileToMol(pathName + "/Issue242-2.mol");
  TEST_ASSERT(mol2);

  TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol2, 30, 2370) >= 0);
  mb1 = MolToMolBlock(*mol);
  mb2 = MolToMolBlock(*mol2);

  //std::cout << mb1 << "------\n";
  //std::cout << mb2 << "------\n";

  field = MMFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  field2 = MMFF::constructForceField(*mol2);
  TEST_ASSERT(field2);
  field2->initialize();
  e1 = field->calcEnergy();
  e2 = field2->calcEnergy();
  BOOST_LOG(rdInfoLog) << "E1: " << e1 << std::endl;
  BOOST_LOG(rdInfoLog) << "E2: " << e2 << std::endl;
  //TEST_ASSERT(feq(e2,e1,0.1));

  needMore = field->minimize(200,1.0e-4);
  needMore = field2->minimize(200,1.0e-4);
  e1 = field->calcEnergy();
  e2 = field2->calcEnergy();
  BOOST_LOG(rdInfoLog) << "E1: " << e1 << std::endl;
  BOOST_LOG(rdInfoLog) << "E2: " << e2 << std::endl;
  TEST_ASSERT(feq(e2, e1, 0.1));

  delete mol;
  delete mol2;
  delete field;
  delete field2;
  

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

void testUFFMultiThread(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Test UFF multithreading" << std::endl;

  ForceFields::ForceField *field;

  std::string pathName = getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
  SDMolSupplier suppl(pathName + "/bulk.sdf");
  std::vector<ROMol *> mols;
  while(!suppl.atEnd()&&mols.size()<100){
    ROMol *mol=0;
    try{
      mol=suppl.next();
    } catch(...){
      continue;
    }
    if(!mol) continue;
    mols.push_back(mol);
  }

  std::cerr<<"generating reference data"<<std::endl;
  std::vector<double> energies(mols.size(),0.0);
  for(unsigned int i=0;i<mols.size();++i){
    ROMol mol(*mols[i]);
    ForceFields::ForceField *field = 0;
    try {
      field = UFF::constructForceField(mol);
    } catch (...) {
      field = 0;
    }
    TEST_ASSERT(field);
    field->initialize();
    int failed = field->minimize(500);
    TEST_ASSERT(!failed);
    energies[i]=field->calcEnergy();
    delete field;
  }
  
  boost::thread_group tg;

  std::cerr<<"processing"<<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_uff,mols,energies,count,i));
  }
  tg.join_all();
  
  BOOST_FOREACH(ROMol *mol,mols){
    delete mol;
  }
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testCrippenO3AConstraints() {
  ROMol *m = SmilesToMol("n1ccc(cc1)-c1ccccc1");
  TEST_ASSERT(m);
  ROMol *m1 = MolOps::addHs(*m);
  delete m;
  TEST_ASSERT(m1);
  DGeomHelpers::EmbedMolecule(*m1);
  MMFF::sanitizeMMFFMol((RWMol &)(*m1));
  MMFF::MMFFMolProperties mp(*m1);
  TEST_ASSERT(mp.isValid());
  ForceFields::ForceField *field = MMFF::constructForceField(*m1, &mp);
  field->initialize();
  field->minimize();
  RWMol *patt = SmartsToMol("nccc-cccc");
  MatchVectType matchVect;
  TEST_ASSERT(SubstructMatch(*m1, (ROMol &)*patt, matchVect));
  unsigned int nIdx = matchVect[0].second;
  unsigned int cIdx = matchVect[matchVect.size() - 1].second;
  MolTransforms::setDihedralDeg(m1->getConformer(), matchVect[2].second,
    matchVect[3].second, matchVect[4].second, matchVect[5].second, 0.0);
  ROMol m2(*m1);
  MolAlign::randomTransform(m2);
  ROMol m3(m2);
  unsigned int prbNAtoms = m2.getNumAtoms();
  std::vector<double> prbLogpContribs(prbNAtoms);
  std::vector<double> prbMRContribs(prbNAtoms);
  std::vector<unsigned int> prbAtomTypes(prbNAtoms);
  std::vector<std::string> prbAtomTypeLabels(prbNAtoms);
  Descriptors::getCrippenAtomContribs(m2, prbLogpContribs,
    prbMRContribs, true, &prbAtomTypes, &prbAtomTypeLabels);
  MolAlign::O3A *o3a = new MolAlign::O3A(m2, *m1,
    &prbLogpContribs, &prbLogpContribs, MolAlign::O3A::CRIPPEN);
  TEST_ASSERT(o3a);
  o3a->align();
  delete o3a;
  double d = (m2.getConformer().getAtomPos(cIdx)
    - m1->getConformer().getAtomPos(cIdx)).length();
  TEST_ASSERT(feq(d, 0.0, 1));
  MatchVectType constraintMap;
  constraintMap.push_back(std::make_pair(cIdx, nIdx));
  o3a = new MolAlign::O3A(m3, *m1, &prbLogpContribs, &prbLogpContribs,
    MolAlign::O3A::CRIPPEN, -1, -1, false, 50, 0, &constraintMap);
  TEST_ASSERT(o3a);
  o3a->align();
  delete o3a;
  d = (m3.getConformer().getAtomPos(cIdx)
    - m1->getConformer().getAtomPos(cIdx)).length();
  TEST_ASSERT(feq(d, 7.0, 1.0));
  delete m1;
}

 int MMFFOptimizeMolecule(ROMol &mol, std::string mmffVariant = "MMFF94",
   int maxIters = 200, double nonBondedThresh = 100.0, int confId = -1,
   bool ignoreInterfragInteractions = true)
 {
   int res = -1;
   
   MMFF::MMFFMolProperties mmffMolProperties(mol, mmffVariant);
   if (mmffMolProperties.isValid()) {
     ForceFields::ForceField *ff = MMFF::constructForceField(mol,
       &mmffMolProperties, nonBondedThresh, confId, ignoreInterfragInteractions);
     ff->initialize();
     res = ff->minimize(maxIters);
     delete ff;
   }
   
   return res;
 }

void testGithub308()
{
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing github 308: crash during MMFF parameterization ." << std::endl;
  ROMol *mol = SmilesToMol("FF");
  TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol) >= 0);
  int needMore;
  ForceFields::ForceField *field = 0;
  TEST_ASSERT(mol);
  MMFF::MMFFMolProperties mmffMolProperties(*mol);
  TEST_ASSERT(mmffMolProperties.isValid());
  field = MMFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  needMore = field->minimize(200, 1.0e-6, 1.0e-3);
  TEST_ASSERT(!needMore);
}

void testSFIssue1653802(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing SFIssue1653802." << std::endl;

  RWMol *mol;
  int needMore;
  ForceFields::ForceField *field;

  std::string pathName=getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";

  mol = MolFileToMol(pathName+"/cyclobutadiene.mol",false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);


  UFF::AtomicParamVect types;
  bool foundAll;
  boost::shared_array<boost::uint8_t> nbrMat;
  boost::tie(types,foundAll)=UFF::getAtomTypes(*mol);
  TEST_ASSERT(foundAll);
  TEST_ASSERT(types.size()==mol->getNumAtoms());
  field=new ForceFields::ForceField();
  UFF::Tools::addBonds(*mol,types,field);
  TEST_ASSERT(field->contribs().size()==8);

  nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
  UFF::Tools::addAngles(*mol,types,field);
  TEST_ASSERT(field->contribs().size()==20);
  UFF::Tools::addTorsions(*mol,types,field);
  //std::cout << field->contribs().size() << std::endl;
  TEST_ASSERT(field->contribs().size()==36);
  UFF::Tools::addNonbonded(*mol,0,types,field,nbrMat);
  delete field;

  field = UFF::constructForceField(*mol);
  field->initialize();
  needMore = field->minimize(200,1e-6,1e-3);
  TEST_ASSERT(!needMore);
  
  delete mol;
  delete field;
  BOOST_LOG(rdErrorLog) << "  done" << std::endl;
}

void testMMFFBatch() {
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog)
      << "    Testing bulk MMFF (regression to check that things run)."
      << std::endl;

  ROMol *mol;

  ForceFields::ForceField *field;

  std::string pathName = getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";
  SDMolSupplier suppl(pathName + "/bulk.sdf");

  int count = 0;
  mol = suppl.next();
  while (mol && (!(suppl.atEnd()))) {
    ++count;
    std::string origMolBlock = MolToMolBlock(*mol);

    BOOST_LOG(rdErrorLog) << "Mol:" << count << std::endl;
    try {
      field = MMFF::constructForceField(*mol);
    } catch (...) {
      field = 0;
    }
    if (field) {
      field->initialize();
      int failed = field->minimize(500);
      if (failed) {
        BOOST_LOG(rdErrorLog) << " not converged (code = " << failed << ")"
                              << std::endl;
        std::cout << origMolBlock << "$$$$" << std::endl;
        std::cout << MolToMolBlock(*mol) << "$$$$" << std::endl;
      }
      delete field;
    }
    delete mol;
    mol = suppl.next();
  }

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

void testSFIssue1653802() {
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing SFIssue1653802." << std::endl;

  RWMol *mol;
  int needMore;
  ForceFields::ForceField *field;

  std::string pathName = getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/MMFF/test_data";

  mol = MolFileToMol(pathName + "/cyclobutadiene.mol", false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);
  MMFF::MMFFMolProperties *mmffMolProperties =
      new MMFF::MMFFMolProperties(*mol);
  TEST_ASSERT(mmffMolProperties);

  boost::shared_array<boost::uint8_t> nbrMat;
  field = new ForceFields::ForceField();
  MMFF::Tools::addBonds(*mol, mmffMolProperties, field);
  TEST_ASSERT(field->contribs().size() == 8);

  nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
  MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
  TEST_ASSERT(field->contribs().size() == 20);
  MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
  // std::cout << field->contribs().size() << std::endl;
  TEST_ASSERT(field->contribs().size() == 36);
  MMFF::Tools::addVdW(*mol, 0, mmffMolProperties, field, nbrMat);
  delete field;

  field = MMFF::constructForceField(*mol);
  field->initialize();
  needMore = field->minimize(200, 1.0e-6, 1.0e-3);
  TEST_ASSERT(!needMore);

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

void testGitHubIssue62() {
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing GitHubIssue62." << std::endl;

  std::string pathName=getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
  {
    double energyValues[] =
      { 38.687, 174.698, 337.986, 115.248,
        2.482, 1.918, 10.165, 98.469, 39.078,
        267.236, 15.747, 202.121, 205.539,
        20.044, 218.986, 79.627 };
    SmilesMolSupplier smiSupplier(pathName + "/Issue62.smi");
    SDWriter *sdfWriter = new SDWriter(pathName + "/Issue62.sdf");
    for (unsigned int i = 0; i < smiSupplier.length(); ++i) {
      ROMol *mol = MolOps::addHs(*(smiSupplier[i]));
      TEST_ASSERT(mol);
      std::string molName = "";
      if (mol->hasProp(common_properties::_Name)) {
        mol->getProp(common_properties::_Name, molName);
      }
      DGeomHelpers::EmbedMolecule(*mol);
      ForceFields::ForceField *field = UFF::constructForceField(*mol);
      TEST_ASSERT(field);
      field->initialize();
      int needMore = field->minimize(200, 1.e-6, 1.e-3);
      TEST_ASSERT(!needMore);
      sdfWriter->write(*mol);
      double e = field->calcEnergy();
      BOOST_LOG(rdErrorLog) << molName << " " << e << std::endl;
      TEST_ASSERT(fabs(e - energyValues[i]) < 1.);
    }
    sdfWriter->close();
    BOOST_LOG(rdErrorLog) << "  done" << std::endl;
  }
}

void testUFFBuilder2(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing UFF builder+minimization." << std::endl;

  RWMol *mol;
  std::string key;
  int needMore;

  ForceFields::ForceField *field;

  std::string pathName=getenv("RDBASE");
  pathName += "/Code/GraphMol/ForceFieldHelpers/UFF/test_data";
  mol = MolFileToMol(pathName+"/small1.mol",false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);

  field=UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  needMore = field->minimize();
  TEST_ASSERT(!needMore);
  //std::cout << MolToMolBlock(mol);
  delete mol;
  delete field;

  mol = MolFileToMol(pathName+"/small2.mol",false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);

  field=UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  needMore = field->minimize(150);
  TEST_ASSERT(!needMore);
  //std::cout << MolToMolBlock(mol);
  delete mol;
  delete field;

  mol = MolFileToMol(pathName+"/benzene.mol",false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);

  field=UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  needMore = field->minimize();
  TEST_ASSERT(!needMore);
  //std::cout << MolToMolBlock(mol);
  delete mol;
  delete field;
  
  mol = MolFileToMol(pathName+"/toluene.mol",false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);

  field=UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  needMore = field->minimize();
  TEST_ASSERT(!needMore);
  //std::cout << MolToMolBlock(mol);
  delete mol;
  delete field;

  mol = MolFileToMol(pathName+"/complex1.mol",false);
  TEST_ASSERT(mol);
  MolOps::sanitizeMol(*mol);

  field=UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  needMore = field->minimize();
  TEST_ASSERT(!needMore);
  //std::cout << MolToMolBlock(mol);
  delete mol;
  delete field;

  

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

void testTorsionAngleM6() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << " Test CrystalFF torsional term." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1, p2, p3, p4;
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);
  ps.push_back(&p3);
  ps.push_back(&p4);

  ForceFields::CrystalFF::TorsionAngleContribM6 *contrib;
  // ------- ------- ------- ------- ------- ------- -------
  // Basic SP3 - SP3
  // ------- ------- ------- ------- ------- ------- -------

  // [!#1:1][CX4H2:2][email protected][CX4H2:3][!#1:4] 1 0.0 1 0.0 1 4.0 1 0.0 1 0.0 1 0.0
  std::vector<int> signs(6, 1);
  std::vector<double> v(6, 0.0);
  v[2] = 4.0;

  contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(&ff, 0, 1, 2, 3,
                                                              v, signs);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  p1.x = 0;
  p1.y = 1.5;
  p1.z = 0;

  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;

  p3.x = 1.5;
  p3.y = 0.0;
  p3.z = 0.0;

  p4.x = 1.5;
  p4.y = 0.0;
  p4.z = 1.5;

  ff.initialize();
  ff.minimize(10, 1e-8, 1e-8);
  double cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
      *(RDGeom::Point3D *)ff.positions()[0],
      *(RDGeom::Point3D *)ff.positions()[1],
      *(RDGeom::Point3D *)ff.positions()[2],
      *(RDGeom::Point3D *)ff.positions()[3]);
  TEST_ASSERT(RDKit::feq(cosPhi, 0.5, 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // Basic SP2 - SP2
  // ------- ------- ------- ------- ------- ------- -------

  signs[1] = -1;
  v[2] = 0.0;
  v[1] = 7.0;

  ff.contribs().pop_back();
  contrib = new ForceFields::CrystalFF::TorsionAngleContribM6(&ff, 0, 1, 2, 3,
                                                              v, signs);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  p1.x = 0;
  p1.y = 1.5;
  p1.z = 0.1;

  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;

  p3.x = 1.5;
  p3.y = 0.0;
  p3.z = 0.0;

  p4.x = 1.5;
  p4.y = 0.2;
  p4.z = 1.5;

  ff.initialize();
  ff.minimize(10, 1e-8, 1e-8);
  cosPhi = ForceFields::MMFF::Utils::calcTorsionCosPhi(
      *(RDGeom::Point3D *)ff.positions()[0],
      *(RDGeom::Point3D *)ff.positions()[1],
      *(RDGeom::Point3D *)ff.positions()[2],
      *(RDGeom::Point3D *)ff.positions()[3]);
  TEST_ASSERT(RDKit::feq(cosPhi, 1.0, 1e-4));
}