C++ OBMol::Has3D方法代码示例

extern "C" int
ob_3D (char *molfile)
{
  OBMol mol;
  OBConversion conv;
  string tmpStr (molfile);
  istringstream molstream (tmpStr);
  int threed = 0;

  conv.SetInAndOutFormats ("MDL", "MDL");

  conv.Read (&mol, &molstream);

  if (mol.Has3D ())
    threed++;

  return (threed);
}

bool OBReader::readSmiString(QString smiString)
{
    using namespace OpenBabel;

    OBConversion conv;

    if (!conv.SetInFormat("smi"))
    {
        qDebug() << "Error in conv.SetInFormat().";
        return false;
    }

    OBMol obMol;

    if (!conv.ReadString(&obMol, smiString.toStdString()))
    {
        qDebug() << "Error occured while reading the smi string.";
        return false;
    }

    if (!obMol.Has3D())
    {
        if (!buildGeometry(&obMol))
        {
            qDebug() << "Error in buildGeometry()";
            return false;
        }
    }

    if (!toMolecule(&obMol))
    {
        qDebug() << "Could not convert OBMol to Molecule.";
        return false;
    }


    return true;
}

bool OBReader::readFile(QString fileName)
{
    using namespace OpenBabel;

    OBConversion conv;

    OBFormat *format = conv.FormatFromExt(fileName.toStdString());

    if (!format || !conv.SetInFormat(format))
    {
        qDebug() << "Unsupported File Format.";
        return false;
    }

    std::ifstream ifs;
    ifs.open(fileName.toStdString());

    if (!ifs)
    {
        qDebug() << "Could not open the file.";
        return false;
    }

    OBMol obMol;
    if (!conv.Read(&obMol, &ifs))
    {
        qDebug() << "Error occured while reading the file.";
        return false;
    }

    if (!obMol.Has3D())
    {
        static bool showMsgBox = true;
        if (showMsgBox)
        {
            QMessageBox msgBox;
            msgBox.setWindowTitle(tr("OBReader"));
            msgBox.setText(tr("No 3D coordinate values present in this file."));
            msgBox.setInformativeText(tr("OBReader will generate the rough molecular geometry."));
            msgBox.setCheckBox(new QCheckBox(tr("Don’t show this message again.")));
            msgBox.setIcon(QMessageBox::Information);
            msgBox.exec();

            showMsgBox = !msgBox.checkBox()->isChecked();
        }

        if (!buildGeometry(&obMol))
        {
            qDebug() << "Error in buildGeometry()";
            return false;
        }
    }

    if (!toMolecule(&obMol))
    {
        qDebug() << "Could not convert OBMol to Molecule.";
        return false;
    }

    return true;
}

int main(int argc,char *argv[])
{
  // turn off slow sync with C-style output (we don't use it anyway).
  std::ios::sync_with_stdio(false);

  OBConversion conv;
  OBFormat *inFormat, *canFormat;
  OBMol mol;
  ifstream ifs;
  vector<OBMol> fragments;
  unsigned int fragmentCount = 0; // track how many in library -- give a running count
  map<string, int> index; // index of cansmi
  string currentCAN;
  unsigned int size;
  OBAtom *atom;
  OBBond *bond;
  bool nonRingAtoms, nonRingBonds;
  char buffer[BUFF_SIZE];

  canFormat = conv.FindFormat("can");
  conv.SetOutFormat(canFormat);

  if (argc < 2)
    {
      cout << "Usage: obfragment <file>" << endl;
      return(-1);
    }

  for (int i = 1; i < argc; i++) {
    cerr << " Reading file " << argv[i] << endl;

    inFormat = conv.FormatFromExt(argv[i]);
    if(inFormat==NULL || !conv.SetInFormat(inFormat))
      {
        cerr << " Cannot read file format for " << argv[i] << endl;
        continue; // try next file
      }
    
    ifs.open(argv[i]);
    
    if (!ifs)
      {
        cerr << "Cannot read input file: " << argv[i] << endl;
        continue;
      }
    
    
    while(ifs.peek() != EOF && ifs.good())
      {
        conv.Read(&mol, &ifs);
        if (!mol.Has3D()) continue; // invalid coordinates!
        mol.DeleteHydrogens(); // remove these before we do anything else
        
        do {
          nonRingAtoms = false;
          size = mol.NumAtoms();
          for (unsigned int i = 1; i <= size; ++i)
            {
              atom = mol.GetAtom(i);
              if (!atom->IsInRing()) {
                mol.DeleteAtom(atom);
                nonRingAtoms = true;
                break; // don't know how many atoms there are
              } 
              // Previously, we changed atoms to carbon here.
              // Now we perform this alchemy in terms of string-rewriting
              // once the canonical SMILES is generated
            }
        } while (nonRingAtoms);
        
        if (mol.NumAtoms() < 3)
          continue;
        
        if (mol.NumBonds() == 0)
          continue;
        
        do {
          nonRingBonds = false;
          size = mol.NumBonds();
          for (unsigned int i = 0; i < size; ++i)
            {
              bond = mol.GetBond(i);
              if (!bond->IsInRing()) {
                mol.DeleteBond(bond);
                nonRingBonds = true;
                break; // don't know how many bonds there are
              }
            }        
        } while (nonRingBonds);

        fragments = mol.Separate();
        for (unsigned int i = 0; i < fragments.size(); ++i)
          {
            if (fragments[i].NumAtoms() < 3) // too small to care
              continue;
              
            currentCAN = conv.WriteString(&fragments[i], true);
            currentCAN = RewriteSMILES(currentCAN); // change elements to "a/A" for compression
            if (index.find(currentCAN) != index.end()) { // already got this
              index[currentCAN] += 1; // add to the count for bookkeeping
//.........这里部分代码省略.........

  //! Calculate the signed volume for an atom.  If the atom has a valence of 3
  //! the coordinates of an attached hydrogen are calculated
  //! Puts attached Hydrogen last at the moment, like mol V3000 format.
  //! If ReZero=false (the default is true) always make pseudo z coords and leave them in mol
  double CalcSignedVolume(OBMol &mol,OBAtom *atm, bool ReZeroZ)
  {
    vector3 tmp_crd;
    vector<unsigned int> nbr_atms;
    vector<vector3> nbr_crds;
    bool use_central_atom = false,is2D=false;
    //   double hbrad = etab.CorrectedBondRad(1,0);
           
    if (!ReZeroZ || !mol.Has3D()) //give pseudo Z coords if mol is 2D
      {
        vector3 v,vz(0.0,0.0,1.0);
        is2D = true;
        OBAtom *nbr;
        OBBond *bond;
        vector<OBBond*>::iterator i;
        for (bond = atm->BeginBond(i);bond;bond = atm->NextBond(i))
          {
            nbr = bond->GetEndAtom();
            if (nbr != atm)
              {
                v = nbr->GetVector();
                if (bond->IsWedge())
                  v += vz;
                else
                  if (bond->IsHash())
                    v -= vz;

                nbr->SetVector(v);
              }
            else
              {
                nbr = bond->GetBeginAtom();
                v = nbr->GetVector();
                if (bond->IsWedge())
                  v -= vz;
                else
                  if (bond->IsHash())
                    v += vz;

                nbr->SetVector(v);
              }
          }
      }
    
    if (atm->GetHvyValence() < 3)
      {
        stringstream errorMsg;
        errorMsg << "Cannot calculate a signed volume for an atom with a heavy atom valence of " << atm->GetHvyValence() << endl;
        obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo);
        return(0.0);
      }

    // Create a vector with the coordinates of the neighbor atoms
    // Also make a vector with Atom IDs
    OBAtom *nbr;
    vector<OBBond*>::iterator bint;
    for (nbr = atm->BeginNbrAtom(bint);nbr;nbr = atm->NextNbrAtom(bint))
      {
        nbr_atms.push_back(nbr->GetIdx());
      }
    // sort the neighbor atoms to insure a consistent ordering
    sort(nbr_atms.begin(),nbr_atms.end());
    for (unsigned int i = 0; i < nbr_atms.size(); ++i)
      {
        OBAtom *tmp_atm = mol.GetAtom(nbr_atms[i]);
        nbr_crds.push_back(tmp_atm->GetVector());
      }
    /*
    // If we have three heavy atoms we need to calculate the position of the fourth
    if (atm->GetHvyValence() == 3)
    {
    double bondlen = hbrad+etab.CorrectedBondRad(atm->GetAtomicNum(),atm->GetHyb());
    atm->GetNewBondVector(tmp_crd,bondlen);
    nbr_crds.push_back(tmp_crd);
    }
    */
    for(unsigned int j=0;j < nbr_crds.size();++j) // Checks for a neighbour having 0 co-ords (added hydrogen etc)
      {
        // are the coordinates zero to 6 or more significant figures
        if (nbr_crds[j].IsApprox(VZero, 1.0e-6) && use_central_atom==false)
          use_central_atom=true;
        else if (nbr_crds[j].IsApprox(VZero, 1.0e-6))
          {
            obErrorLog.ThrowError(__FUNCTION__, "More than 2 neighbours have 0 co-ords when attempting 3D chiral calculation", obInfo);
          }
      }

    // If we have three heavy atoms we can use the chiral center atom itself for the fourth
    // will always give same sign (for tetrahedron), magnitude will be smaller.
    if(nbr_atms.size()==3 || use_central_atom==true)
      {
        nbr_crds.push_back(atm->GetVector());
        nbr_atms.push_back(mol.NumAtoms()+1); // meed to add largest number on end to work
      }
    OBChiralData* cd=(OBChiralData*)atm->GetData(OBGenericDataType::ChiralData); //Set the output atom4refs to the ones used
    if(cd==NULL)
//.........这里部分代码省略.........