C++ OBMol::GetAllData方法代码示例

void testTetrahedralStereo1()
{
  cout << "testTetrahedralStereo1()" << endl;
  // read a smiles string
  OBMol mol;
  OBConversion conv;
  OB_REQUIRE( conv.SetInFormat("smi") );
  cout << "smiles: C[[email protected]](O)N" << endl;
  OB_REQUIRE( conv.ReadString(&mol, "C[[email protected]](O)N") );

  // get the stereo data
  OB_REQUIRE( mol.HasData(OBGenericDataType::StereoData) );
  std::vector<OBGenericData *> stereoData = mol.GetAllData(OBGenericDataType::StereoData);
  OB_REQUIRE( stereoData.size() == 1 );

  // convert to tetrahedral data
  OB_REQUIRE( ((OBStereoBase*)stereoData[0])->GetType() == OBStereo::Tetrahedral );
  OBTetrahedralStereo *ts = dynamic_cast<OBTetrahedralStereo*>(stereoData[0]);
  OB_REQUIRE( ts );

  // print the configuration
  cout << *ts << endl;

  // construct a valid configuration here
  //
  // C[[email protected]](O)N
  // 0 1 2  3 4  <- ids
  //
  OBTetrahedralStereo::Config cfg(1, 0, OBStereo::MakeRefs(4, 3, 2), OBStereo::Clockwise);

  // compare stereochemistry
  OB_REQUIRE( ts->GetConfig() == cfg );

  cout << endl;
}

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.........

extern "C" int readgrid_(float *vdata, int *nx, int *ny, int *nz,
  float *x0, float *y0, float *z0, float *xx, float *yy, float *zz,
  char *file, int fsize) {

  float dx,dy,dz;
  int gsize;
  float v, vmin, vmax, vavg;
  int navg = 0;

  OBMol mol;
  OBConversion conv;
  conv.SetInFormat("cube");
 
  std::string fname = file;
  int blank = fname.find(" ");
  //printf("%d,'%s'\n", blank, fname.substr(0,blank).c_str());
  conv.ReadFile(&mol, fname.substr(0,blank).c_str());
  //cout << mol.NumAtoms() << " atoms." << endl;
  if (mol.HasData(OBGenericDataType::GridData)) {
    std::vector<OBGenericData*> grids = mol.GetAllData(OBGenericDataType::GridData);
    OBGridData *grid = dynamic_cast<OBGridData *> (grids[0]);
    gsize = grid->GetNumberOfPoints();
    grid->GetNumberOfPoints(*nx, *ny, *nz);
    vector3 origin = grid->GetOriginVector();
    *x0 = origin[0]; *y0 = origin[1]; *z0 = origin[2];
    vector3 maxv = grid->GetMaxVector();
    *xx = maxv[0]; *yy = maxv[1]; *zz = maxv[2];
    dx=(*xx-*x0)/(*nx-1);
    dy=(*yy-*y0)/(*ny-1);
    dz=(*zz-*z0)/(*nz-1);
    printf("%s %d=%d*%d*%d\n", grid->GetAttribute().c_str(), gsize, *nx, *ny, *nz);
    printf("%f %f\n", grid->GetMinValue(), grid->GetMaxValue());
    printf("%f,%f,%f\n", *x0,*y0,*z0);
    printf("%f,%f,%f\n", *xx,*yy,*zz);
    printf("%f,%f,%f\n", dx,dy,dz);
 
    //vdata = (float *)calloc(gsize, sizeof(float));
/* this is for fortran, so reverse sense of slowest/fastest moving dimensions */
    //for (int i=0; i<*nx; ++i) {
    vmin = grid->GetValue(0,0,0);
    vmax = vmin;
    for (int i=0; i<*nz; ++i) {
      for (int j=0; j<*ny; ++j) {
        //for (int k=0; k<*nz; ++k) {
        for (int k=0; k<*nx; ++k) {
          //*vdata++ = grid->GetValue(i,j,k);
          v = grid->GetValue(k,j,i);
          if (v < 1e30 && v > -1e30) {
            if (v < vmin) vmin = v;
            if (v > vmax) vmax = v;
            ++navg;
            vavg += v;
          } else {
            v = vmax * 1000; // just a guess
          }
          *vdata++ = v;
        }
      }
    }
  }
  vavg = vavg/navg;
  printf("min/avg/max = %f/%f/%f\n", vmin, vavg, vmax);
  return 0;
}