C++ OBBond::IsHash方法代码示例

  //! Sets atom->IsChiral() to true for chiral atoms
  void OBMol::FindChiralCenters()
  {
    if (HasChiralityPerceived())
      return;
    SetChiralityPerceived();

    obErrorLog.ThrowError(__FUNCTION__,
                          "Ran OpenBabel::FindChiralCenters", obAuditMsg);

    //do quick test to see if there are any possible chiral centers
    bool mayHaveChiralCenter=false;
    OBAtom *atom,*nbr;
    vector<OBAtom*>::iterator i;
    for (atom = BeginAtom(i);atom;atom = NextAtom(i))
      if (atom->GetHyb() == 3 && atom->GetHvyValence() >= 3)
        {
          mayHaveChiralCenter=true;
          break;
        }

    if (!mayHaveChiralCenter)
      return;

    OBBond *bond;
    vector<OBBond*>::iterator j;
    for (bond = BeginBond(j);bond;bond = NextBond(j))
      if (bond->IsWedge() || bond->IsHash())
        (bond->GetBeginAtom())->SetChiral();

    vector<unsigned int> vgid;
    GetGIDVector(vgid);
    vector<unsigned int> tlist;
    vector<unsigned int>::iterator k;

    bool ischiral;
    for (atom = BeginAtom(i);atom;atom = NextAtom(i))
      if (atom->GetHyb() == 3 && atom->GetHvyValence() >= 3 && !atom->IsChiral())
        {
          tlist.clear();
          ischiral = true;

          for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
            {
              for (k = tlist.begin();k != tlist.end();++k)
                if (vgid[nbr->GetIdx()-1] == *k)
                  ischiral = false;

              if (ischiral)
                tlist.push_back(vgid[nbr->GetIdx()-1]);

              else
                break;
            }

          if (ischiral)
            atom->SetChiral();
        }
  }

bool ChemDrawXMLFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
    static const xmlChar C_MOLECULE[]         = "fragment";
    static const xmlChar C_CDXML[]            = "CDXML";
    static const xmlChar C_BONDLENGTH[]       = "BondLength";
    static const xmlChar C_PAGE[]             = "page";
    static const xmlChar C_ATOM[]             = "n";
    static const xmlChar C_BOND[]             = "b";
    static const xmlChar C_ID[]               = "id";

    static const xmlChar C_CHARGE[]           = "Charge";
    static const xmlChar C_COORDS[]           = "p";
    static const xmlChar C_ELEMENT[]          = "Element";
    static const xmlChar C_ORDER[]            = "Order";
    static const xmlChar C_BEGIN[]            = "B";
    static const xmlChar C_END[]              = "E";
    static const xmlChar C_DISPLAY[]          = "Display";

    _pxmlConv = XMLConversion::GetDerived(pConv,false);
    if(!_pxmlConv)
        return false;

    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
        return false;
    OBMol &mol = *pmol;

    OBBond *pbond;
    vector<OBBond*>::iterator j;
    if(_pxmlConv->GetOutputIndex() == 1)
    {
        xmlTextWriterStartDocument(writer(), NULL, NULL, NULL);
        xmlTextWriterWriteDTD(writer(), BAD_CAST "CDXML", NULL, BAD_CAST "http://www.camsoft.com/xml/cdxml.dtd", NULL);
        xmlTextWriterStartElement(writer(), C_CDXML);
        xmlTextWriterWriteFormatAttribute(writer(), C_BONDLENGTH , "30");
        xmlTextWriterStartElement(writer(), C_PAGE); // put everything on one page
        // now guess the average bond size for the first molecule and scale to 30.
        _scale = 0.;
        if (mol.NumBonds())
        {
            for (pbond = mol.BeginBond(j); pbond; pbond = mol.NextBond(j))
                _scale += pbond->GetLength();
            _scale /= mol.NumBonds();
        }
        else
            _scale = 1.; // FIXME: what happens if the molecule has no bond?
        _scale = 30. / _scale;
        _offset = 0;
    }

    xmlTextWriterStartElement(writer(), C_MOLECULE);

    OBAtom *patom;
    vector<OBAtom*>::iterator i;
    int n;
    for (patom = mol.BeginAtom(i); patom; patom = mol.NextAtom(i))
    {
        xmlTextWriterStartElement(writer(), C_ATOM);

        xmlTextWriterWriteFormatAttribute(writer(), C_ID , "%d", patom->GetIdx() + _offset);
        xmlTextWriterWriteFormatAttribute(writer(), C_COORDS , "%f %f", patom->GetX() * _scale, patom->GetY() * _scale);
        n = patom->GetAtomicNum();
        if (n != 6)
        {
            xmlTextWriterWriteFormatAttribute(writer(), C_ELEMENT , "%d", n);
        }
        n = patom->GetFormalCharge();
        if (n != 0)
        {
            xmlTextWriterWriteFormatAttribute(writer(), C_CHARGE , "%d", n);
        }
        xmlTextWriterEndElement(writer());
    }

    for (pbond = mol.BeginBond(j); pbond; pbond = mol.NextBond(j))
    {
        xmlTextWriterStartElement(writer(), C_BOND);
        patom = pbond->GetBeginAtom();
        xmlTextWriterWriteFormatAttribute(writer(), C_BEGIN , "%d", patom->GetIdx() + _offset);
        patom = pbond->GetEndAtom();
        xmlTextWriterWriteFormatAttribute(writer(), C_END , "%d", patom->GetIdx() + _offset);
        n = pbond->GetBO();
        if (n != 1)
        {
            xmlTextWriterWriteFormatAttribute(writer(), C_ORDER , "%d", n);
        }
        if (pbond->IsHash())
            xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgeBegin");
        else if (pbond->IsWedge())
            xmlTextWriterWriteFormatAttribute(writer(), C_DISPLAY , "WedgedHashEnd");
        xmlTextWriterEndElement(writer());
    }
    _offset += mol.NumAtoms ();

    xmlTextWriterEndElement(writer());//molecule

    //TODO: Writing property block

    if(_pxmlConv->IsLast())
    {
//.........这里部分代码省略.........

  bool OBDepict::DrawMolecule(OBMol *mol)
  {
    if (!d->painter)
      return false;

    d->mol = mol;

    double width=0.0, height=0.0;

    OBAtom *atom;
    OBBondIterator j;
    OBAtomIterator i;

    if(mol->NumAtoms()>0) {
      // scale bond lengths
      double bondLengthSum = 0.0;
      for (OBBond *bond = mol->BeginBond(j); bond; bond = mol->NextBond(j))
        bondLengthSum += bond->GetLength();
      const double averageBondLength = bondLengthSum / mol->NumBonds();
      const double f = mol->NumBonds() ? d->bondLength / averageBondLength : 1.0;
      for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
        atom->SetVector(atom->GetX() * f, atom->GetY() * f, 0.0);

      // find min/max values
      double min_x, max_x;
      double min_y, max_y;
      atom = mol->BeginAtom(i);
      min_x = max_x = atom->GetX();
      min_y = max_y = atom->GetY();
      for (atom = mol->NextAtom(i); atom; atom = mol->NextAtom(i)) {
        min_x = std::min(min_x, atom->GetX());
        max_x = std::max(max_x, atom->GetX());
        min_y = std::min(min_y, atom->GetY());
        max_y = std::max(max_y, atom->GetY());
      }

      const double margin = 40.0;
      // translate all atoms so the bottom-left atom is at margin,margin
      for (atom = mol->BeginAtom(i); atom; atom = mol->NextAtom(i))
        atom->SetVector(atom->GetX() - min_x + margin, atom->GetY() - min_y + margin, 0.0);

      width  = max_x - min_x + 2*margin;
      height = max_y - min_y + 2*margin;
      
      //d->painter->SetPenWidth(d->penWidth);
      //d->painter->SetPenColor(d->pen));
      //d->painter->SetFillColor(OBColor("black"));
    }

    d->painter->NewCanvas(width, height);
    
    // draw bonds
    if(d->options & genWedgeHash)
      d->SetWedgeAndHash(mol);
    for (OBBond *bond = mol->BeginBond(j); bond; bond = mol->NextBond(j)) {
      OBAtom *begin = bond->GetBeginAtom();
      OBAtom *end = bond->GetEndAtom();

      if((d->options & internalColor) && bond->HasData("color"))
        d->painter->SetPenColor(OBColor(bond->GetData("color")->GetValue()));
      else
        d->painter->SetPenColor(d->bondColor);

      if (bond->IsWedge()) {
        d->DrawWedge(begin, end);
      } else if (bond->IsHash()) {
        d->DrawHash(begin, end);
      } else if (!bond->IsInRing()) {
        d->DrawSimpleBond(begin, end, bond->GetBO());
      }
    }
    
    // draw ring bonds
    std::vector<OBRing*> rings(mol->GetSSSR());
    OBBitVec drawnBonds;
    for (std::vector<OBRing*>::iterator k = rings.begin(); k != rings.end(); ++k) {
      OBRing *ring = *k;
      std::vector<int> indexes = ring->_path;
      vector3 center(VZero);
      for (std::vector<int>::iterator l = indexes.begin(); l != indexes.end(); ++l) {
        center += mol->GetAtom(*l)->GetVector();        
      }
      center /= indexes.size();

      for (unsigned int l = 0; l < indexes.size(); ++l) {
        OBAtom *begin = mol->GetAtom(indexes[l]);
        OBAtom *end;
        if (l+1 < indexes.size())
          end = mol->GetAtom(indexes[l+1]);
        else
          end = mol->GetAtom(indexes[0]);

        OBBond *ringBond = mol->GetBond(begin, end);
        if (drawnBonds.BitIsSet(ringBond->GetId()))
          continue;

        if((d->options & internalColor) && ringBond->HasData("color"))
          d->painter->SetPenColor(OBColor(ringBond->GetData("color")->GetValue()));
        else
          d->painter->SetPenColor(d->bondColor);
//.........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.........