C++ ForceField::contribs方法代码示例

本文整理汇总了C++中forcefields::ForceField::contribs方法的典型用法代码示例。如果您正苦于以下问题：C++ ForceField::contribs方法的具体用法？C++ ForceField::contribs怎么用？C++ ForceField::contribs使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类forcefields::ForceField的用法示例。

在下文中一共展示了ForceField::contribs方法的6个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: ForceField

ForceFields::ForceField *constructForceField(
    const BoundsMatrix &mmat, RDGeom::PointPtrVect &positions,
    const VECT_CHIRALSET &csets, double weightChiral, double weightFourthDim,
    std::map<std::pair<int, int>, double> *extraWeights, double basinSizeTol) {
  unsigned int N = mmat.numRows();
  CHECK_INVARIANT(N == positions.size(), "");
  ForceFields::ForceField *field =
      new ForceFields::ForceField(positions[0]->dimension());
  for (unsigned int i = 0; i < N; i++) {
    field->positions().push_back(positions[i]);
  }

  for (unsigned int i = 1; i < N; i++) {
    for (unsigned int j = 0; j < i; j++) {
      double w = 1.0;
      double l = mmat.getLowerBound(i, j);
      double u = mmat.getUpperBound(i, j);
      bool includeIt = false;
      if (extraWeights) {
        std::map<std::pair<int, int>, double>::const_iterator mapIt;
        mapIt = extraWeights->find(std::make_pair(i, j));
        if (mapIt != extraWeights->end()) {
          w = mapIt->second;
          includeIt = true;
        }
      }
      if (u - l <= basinSizeTol) {
        includeIt = true;
      }
      if (includeIt) {
        DistViolationContrib *contrib =
            new DistViolationContrib(field, i, j, u, l, w);
        field->contribs().push_back(ForceFields::ContribPtr(contrib));
      }
    }
  }

  // now add chiral constraints
  if (weightChiral > 1.e-8) {
    for (VECT_CHIRALSET::const_iterator csi = csets.begin(); csi != csets.end();
         csi++) {
      ChiralViolationContrib *contrib =
          new ChiralViolationContrib(field, csi->get(), weightChiral);
      field->contribs().push_back(ForceFields::ContribPtr(contrib));
    }
  }

  // finally the contribution from the fourth dimension if we need to
  if ((field->dimension() == 4) && (weightFourthDim > 1.e-8)) {
    for (unsigned int i = 1; i < N; i++) {
      FourthDimContrib *contrib =
          new FourthDimContrib(field, i, weightFourthDim);
      field->contribs().push_back(ForceFields::ContribPtr(contrib));
    }
  }
  return field;
}  // constructForceField

开发者ID:Ivanov-Inin，项目名称:rdkit，代码行数:57，代码来源:DistGeomUtils.cpp

示例2: testSFIssue1653802

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;
}

开发者ID:AlexanderSavelyev，项目名称:rdkit，代码行数:44，代码来源:testUFFHelpers.cpp

示例3: testSFIssue1653802

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;
}

开发者ID:connorcoley，项目名称:rdkit，代码行数:42，代码来源:testMMFFHelpers.cpp

示例4: testUFFBuilder1

void testUFFBuilder1(){
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing UFF builder tools." << std::endl;

  ROMol *mol,*mol2;
  std::string key;

  UFF::AtomicParamVect types;
  bool foundAll;
  ForceFields::ForceField *field;
  boost::shared_array<boost::uint8_t> nbrMat;

  mol = SmilesToMol("CC(O)C");
  Conformer *conf = new Conformer(mol->getNumAtoms());
  int cid = static_cast<int>(mol->addConformer(conf, true));
  TEST_ASSERT(mol);
  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()==3);

  nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,0)==UFF::Tools::RELATION_1_X);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,1)==UFF::Tools::RELATION_1_2);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,2)==UFF::Tools::RELATION_1_3);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,3)==UFF::Tools::RELATION_1_3);

  UFF::Tools::addAngles(*mol,types,field);
  TEST_ASSERT(field->contribs().size()==6);

  // there are no non-bonded terms here:
  UFF::Tools::addNonbonded(*mol,cid,types,field,nbrMat);
  TEST_ASSERT(field->contribs().size()==6);

  // and no torsions either, until we add Hs:
  UFF::Tools::addTorsions(*mol,types,field);
  TEST_ASSERT(field->contribs().size()==6);

  delete mol;
  delete field;
  mol = SmilesToMol("CCOC");
  Conformer *conf2 = new Conformer(mol->getNumAtoms());
  cid = static_cast<int>(mol->addConformer(conf2, true));
  TEST_ASSERT(mol);
  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()==3);

  nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,0)==UFF::Tools::RELATION_1_X);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,1)==UFF::Tools::RELATION_1_2);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,2)==UFF::Tools::RELATION_1_3);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,3)==UFF::Tools::RELATION_1_X);

  UFF::Tools::addAngles(*mol,types,field);
  TEST_ASSERT(field->contribs().size()==5);
  UFF::Tools::addNonbonded(*mol,cid,types,field,nbrMat);
  TEST_ASSERT(field->contribs().size()==6);
  UFF::Tools::addTorsions(*mol,types,field);
  TEST_ASSERT(field->contribs().size()==7);



  delete mol;
  delete field;
  mol = SmilesToMol("CO");
  Conformer *conf3 = new Conformer(mol->getNumAtoms());
  cid = static_cast<int>(mol->addConformer(conf3, true));
  TEST_ASSERT(mol);
  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()==1);

  nbrMat = UFF::Tools::buildNeighborMatrix(*mol);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,0)==UFF::Tools::RELATION_1_X);
  TEST_ASSERT(UFF::Tools::getTwoBitCell(nbrMat,1)==UFF::Tools::RELATION_1_2);

  UFF::Tools::addAngles(*mol,types,field);
  TEST_ASSERT(field->contribs().size()==1);
  UFF::Tools::addNonbonded(*mol,cid,types,field,nbrMat);
  TEST_ASSERT(field->contribs().size()==1);
  UFF::Tools::addTorsions(*mol,types,field);
  TEST_ASSERT(field->contribs().size()==1);

  
  mol2 = MolOps::addHs(*mol);
  TEST_ASSERT(mol2->getNumAtoms()==6);
  delete field;
//.........这里部分代码省略.........

开发者ID:AlexanderSavelyev，项目名称:rdkit，代码行数:101，代码来源:testUFFHelpers.cpp

示例5: testTorsionAngleM6

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));
}

开发者ID:ASKCOS，项目名称:rdkit，代码行数:89，代码来源:testCrystalFF.cpp

示例6: testMMFFBuilder1

void testMMFFBuilder1() {
  BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
  BOOST_LOG(rdErrorLog) << "    Testing MMFF builder tools." << std::endl;

  ROMol *mol, *mol2;

  ForceFields::ForceField *field;
  boost::shared_array<boost::uint8_t> nbrMat;

  mol = SmilesToMol("CC(O)C");
  Conformer *conf = new Conformer(mol->getNumAtoms());
  int cid = static_cast<int>(mol->addConformer(conf, true));
  TEST_ASSERT(mol);
  MMFF::MMFFMolProperties *mmffMolProperties =
      new MMFF::MMFFMolProperties(*mol);
  TEST_ASSERT(mmffMolProperties);
  TEST_ASSERT(mmffMolProperties->isValid());
  field = new ForceFields::ForceField();
  MMFF::Tools::addBonds(*mol, mmffMolProperties, field);

  TEST_ASSERT(field->contribs().size() == 3);

  nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
  // the neighbor matrix is an upper triangular matrix
  // position indices are as follows:
  //  0  1  2  3
  //     4  5  6
  //        7  8
  //           9
  TEST_ASSERT(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 1, 1) == 4);
  TEST_ASSERT(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 2, 1) == 5);
  TEST_ASSERT(MMFF::Tools::twoBitCellPos(mol->getNumAtoms(), 1, 2) == 5);
  TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 0) ==
              MMFF::Tools::RELATION_1_X);
  TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 1) ==
              MMFF::Tools::RELATION_1_2);
  TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 2) ==
              MMFF::Tools::RELATION_1_3);
  TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 3) ==
              MMFF::Tools::RELATION_1_3);

  MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
  TEST_ASSERT(field->contribs().size() == 6);

  // there are no non-bonded terms here:
  MMFF::Tools::addVdW(*mol, cid, mmffMolProperties, field, nbrMat);
  TEST_ASSERT(field->contribs().size() == 6);

  // and no torsions either, until we add Hs:
  MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
  TEST_ASSERT(field->contribs().size() == 6);

  delete mol;
  delete field;
  delete mmffMolProperties;
  mol = SmilesToMol("CCOC");
  Conformer *conf2 = new Conformer(mol->getNumAtoms());
  cid = static_cast<int>(mol->addConformer(conf2, true));
  TEST_ASSERT(mol);
  mmffMolProperties = new MMFF::MMFFMolProperties(*mol);
  TEST_ASSERT(mmffMolProperties);
  TEST_ASSERT(mmffMolProperties->isValid());
  field = new ForceFields::ForceField();
  MMFF::Tools::addBonds(*mol, mmffMolProperties, field);

  TEST_ASSERT(field->contribs().size() == 3);

  nbrMat = MMFF::Tools::buildNeighborMatrix(*mol);
  TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 0) ==
              MMFF::Tools::RELATION_1_X);
  TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 1) ==
              MMFF::Tools::RELATION_1_2);
  TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 2) ==
              MMFF::Tools::RELATION_1_3);
  TEST_ASSERT(MMFF::Tools::getTwoBitCell(nbrMat, 3) ==
              MMFF::Tools::RELATION_1_4);

  MMFF::Tools::addAngles(*mol, mmffMolProperties, field);
  TEST_ASSERT(field->contribs().size() == 5);
  MMFF::Tools::addVdW(*mol, cid, mmffMolProperties, field, nbrMat);
  TEST_ASSERT(field->contribs().size() == 6);
  MMFF::Tools::addTorsions(*mol, mmffMolProperties, field);
  TEST_ASSERT(field->contribs().size() == 7);

  delete mol;
  delete field;
  delete mmffMolProperties;
  mol = SmilesToMol("CO");
  Conformer *conf3 = new Conformer(mol->getNumAtoms());
  cid = static_cast<int>(mol->addConformer(conf3, true));
  TEST_ASSERT(mol);
  mmffMolProperties = new MMFF::MMFFMolProperties(*mol);
  TEST_ASSERT(mmffMolProperties);
  TEST_ASSERT(mmffMolProperties->isValid());

  field = new ForceFields::ForceField();
  MMFF::Tools::addBonds(*mol, mmffMolProperties, field);

  TEST_ASSERT(field->contribs().size() == 1);

//.........这里部分代码省略.........

开发者ID:connorcoley，项目名称:rdkit，代码行数:101，代码来源:testMMFFHelpers.cpp

注：本文中的forcefields::ForceField::contribs方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。