C++ OBMol::GetAtomById方法代码示例

本文整理汇总了C++中OBMol::GetAtomById方法的典型用法代码示例。如果您正苦于以下问题：C++ OBMol::GetAtomById方法的具体用法？C++ OBMol::GetAtomById怎么用？C++ OBMol::GetAtomById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OBMol的用法示例。

在下文中一共展示了OBMol::GetAtomById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: testIdsAddAtom

void testIdsAddAtom()
{
  OBMol mol;
  // add 5 atoms
  for (int i = 0; i < 5; ++i)
    mol.NewAtom();

  OBAtom a;
  a.SetAtomicNum(6);
  // add a sixth atom
  mol.AddAtom(a);

  OB_REQUIRE( mol.NumAtoms() == 6 );
  OB_REQUIRE( mol.GetAtomById(5) );
  OB_REQUIRE( mol.GetAtomById(5)->GetId() == 5 );
}

开发者ID:Antipina，项目名称:OpenBabel-BFGS，代码行数:16，代码来源:uniqueidtest.cpp

示例2: testIdsNewAtom1

// OBMol::NewAtom()
void testIdsNewAtom1()
{
  OBMol mol;
  for (int i = 0; i < 10; ++i) {
    OBAtom *atom = mol.NewAtom();
    OB_REQUIRE(atom->GetId() == i);
  }

  OB_REQUIRE( mol.GetAtomById(0) );
  OB_REQUIRE( mol.GetAtomById(4) );
  OB_REQUIRE( mol.GetAtomById(9) );
  OB_REQUIRE( !mol.GetAtomById(10) );

  OB_REQUIRE( mol.GetAtomById(0)->GetId() == 0 );
  OB_REQUIRE( mol.GetAtomById(4)->GetId() == 4 );
  OB_REQUIRE( mol.GetAtomById(9)->GetId() == 9 );
}

开发者ID:Antipina，项目名称:OpenBabel-BFGS，代码行数:18，代码来源:uniqueidtest.cpp

示例3: testIdsDeleteAtom

void testIdsDeleteAtom()
{
  OBMol mol;
  for (int i = 0; i < 10; ++i)
    mol.NewAtom();

  OB_REQUIRE( mol.GetAtomById(3) );
  OB_REQUIRE( mol.GetAtomById(4) );
  OB_REQUIRE( mol.GetAtomById(5) );

  mol.DeleteAtom(mol.GetAtomById(4));

  OB_REQUIRE( mol.GetAtomById(3) );
  OB_REQUIRE( mol.GetAtomById(3)->GetId() == 3 );
  OB_REQUIRE( !mol.GetAtomById(4) );
  OB_REQUIRE( mol.GetAtomById(5) );
  OB_REQUIRE( mol.GetAtomById(5)->GetId() == 5 );
}

开发者ID:Antipina，项目名称:OpenBabel-BFGS，代码行数:18，代码来源:uniqueidtest.cpp

示例4: testIdsNewAtom2

// OBMol::NewAtom(unsigned long id)
void testIdsNewAtom2()
{
  OBMol mol;
  for (int i = 0; i < 10; ++i) {
    OBAtom *atom = mol.NewAtom(i*2);
    OB_REQUIRE(atom->GetId() == i*2);
  }

  OB_REQUIRE( mol.GetAtomById(0) );
  OB_REQUIRE( !mol.GetAtomById(7) );
  OB_REQUIRE( mol.GetAtomById(8) );
  OB_REQUIRE( !mol.GetAtomById(9) );
  OB_REQUIRE( mol.GetAtomById(18) );
  OB_REQUIRE( !mol.GetAtomById(19) );

  OB_REQUIRE( mol.GetAtomById(0)->GetId() == 0 );
  OB_REQUIRE( mol.GetAtomById(8)->GetId() == 8 );
  OB_REQUIRE( mol.GetAtomById(18)->GetId() == 18 );
}

开发者ID:Antipina，项目名称:OpenBabel-BFGS，代码行数:20，代码来源:uniqueidtest.cpp

示例5: DeleteExpandedAtoms

void AliasData::DeleteExpandedAtoms(OBMol& mol)
{
  //The atom that carries the AliasData object remains as an Xx atom with no charge;
  //the others are deleted. All the attached hydrogens are also deleted.
  for(unsigned i=0;i<_expandedatoms.size();++i)
  {
    OBAtom* at = mol.GetAtomById(_expandedatoms[i]);
    if(!at)
      continue;
    mol.DeleteHydrogens(at);
    if(at->HasData(AliasDataType))
    {
      at->SetAtomicNum(0);
      at->SetFormalCharge(0);
      at->SetSpinMultiplicity(0);
    }
    else
      mol.DeleteAtom(at);
  }
  _expandedatoms.clear();
}

开发者ID:AlbertDeFusco，项目名称:openbabel，代码行数:21，代码来源:alias.cpp

示例6: genericSmilesCanonicalTest

void genericSmilesCanonicalTest(const std::string &smiles)
{
  cout << "Testing generic smiles <-> canonical smiles" << endl;
  // read a smiles string
  OBMol mol;
  OBConversion conv;
  OB_REQUIRE( conv.SetInFormat("smi") );
  OB_REQUIRE( conv.SetOutFormat("can") );
  cout << "smiles: " << smiles << endl;
  // read a smiles string
  OB_REQUIRE( conv.ReadString(&mol, smiles) );

  // store the stereo data for the smiles string using unique symmetry ids
  std::vector<OBTetrahedralStereo::Config> tetrahedral1;
  std::vector<OBCisTransStereo::Config> cistrans1;
  std::vector<OBSquarePlanarStereo::Config> squareplanar1;

  // get the stereo data
  OB_ASSERT( mol.HasData(OBGenericDataType::StereoData) );
  std::vector<OBGenericData *> stereoData = mol.GetAllData(OBGenericDataType::StereoData);

  std::vector<unsigned int> canlbls;
  std::vector<unsigned int> symclasses;
  OBGraphSym gs1(&mol);
  gs1.GetSymmetry(symclasses);
  CanonicalLabels(&mol, symclasses, canlbls);
  cout << "mol.NumAtoms = " << mol.NumAtoms() << endl;
  for (std::vector<OBGenericData*>::iterator data = stereoData.begin(); data != stereoData.end(); ++data) {
    if (((OBStereoBase*)*data)->GetType() == OBStereo::Tetrahedral) {
      // convert to tetrahedral data
      OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(*data);
      OB_REQUIRE( ts );
      OB_ASSERT( ts->IsValid() );
      if (!ts->IsValid())
        continue;

      OBTetrahedralStereo::Config config = ts->GetConfig();
      // convert atom ids to symmetry ids
     if (mol.GetAtomById(config.center))
        config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
      if (mol.GetAtomById(config.from))
        config.from = canlbls.at( mol.GetAtomById(config.from)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      tetrahedral1.push_back(config);
    } else
    if (((OBStereoBase*)*data)->GetType() == OBStereo::CisTrans) {
      // convert to tetrahedral data
      OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
      OB_REQUIRE( ct );
      OB_ASSERT( ct->IsValid() );

      OBCisTransStereo::Config config = ct->GetConfig();
      // convert atom ids to symmetry ids
      config.begin = canlbls.at( mol.GetAtomById(config.begin)->GetIdx() - 1 );
      config.end = canlbls.at( mol.GetAtomById(config.end)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[3]))
        config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      cistrans1.push_back(config);
    } else
    if (((OBStereoBase*)*data)->GetType() == OBStereo::SquarePlanar) {
      // convert to tetrahedral data
      OBSquarePlanarStereo *sp = dynamic_cast<OBSquarePlanarStereo*>(*data);
      OB_REQUIRE( sp );
      OB_ASSERT( sp->IsValid() );
      if (!sp->IsValid())
        continue;

      OBSquarePlanarStereo::Config config = sp->GetConfig();
      // convert atom ids to symmetry ids
     if (mol.GetAtomById(config.center))
        config.center = canlbls.at( mol.GetAtomById(config.center)->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[0]))
        config.refs[0] = canlbls.at( mol.GetAtomById(config.refs[0])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[1]))
        config.refs[1] = canlbls.at( mol.GetAtomById(config.refs[1])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[2]))
        config.refs[2] = canlbls.at( mol.GetAtomById(config.refs[2])->GetIdx() - 1 );
      if (mol.GetAtomById(config.refs[3]))
        config.refs[3] = canlbls.at( mol.GetAtomById(config.refs[3])->GetIdx() - 1 );
      cout << "Config with symmetry ids: " << config << endl;
      squareplanar1.push_back(config);
    }


  }

  // write to can smiles
//.........这里部分代码省略.........

开发者ID:Acpharis，项目名称:openbabel，代码行数:101，代码来源:smilestest.cpp

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