C++ OBBond::SetBO方法代码示例

//.........这里部分代码省略.........

        if ( !vs.empty() && vs.size() > 0)
          sscanf(buffer,"%i%*s",&natoms);

        if (natoms == 0)
          return false;

        if ( !vs.empty() && vs.size() > 1)
          mol.SetTitle(vs[1]);
        else
          {
            string s = defaultTitle;
            mol.SetTitle(defaultTitle);
          }
      }
    else
      return(false);

    mol.BeginModify();
    mol.ReserveAtoms(natoms);
    connections.resize(natoms+1);

    /***********************************************************************/

    // Get Type Bonds, BondOrder, X, Y, Z

    double x,y,z;
    vector3 v;
    char temp_type[10];
    int i,j;
    double charge;
    OBAtom atom;

    ttab.SetFromType("MMD");
    for (i = 1; i <= natoms; i++)
      {
        if (!ifs.getline(buffer,BUFF_SIZE))
          break;

        int end[6], order[6];

        sscanf(buffer,"%9s%d%d%d%d%d%d%d%d%d%d%d%d%lf%lf%lf",
               temp_type,&end[0],&order[0],&end[1],&order[1],&end[2],&order[2],
               &end[3], &order[3], &end[4], &order[4], &end[5], &order[5],
               &x, &y, &z);

        pair<int,int> tmp;
        for ( j = 0 ; j <=5 ; j++ )
          {
            if ( end[j] > 0  && end[j] > i)
              {
                tmp.first = end[j];
                tmp.second = order[j];
                connections[i].push_back(tmp);
              }
          }

        v.SetX(x);
        v.SetY(y);
        v.SetZ(z);
        atom.SetVector(v);

        string str = temp_type,str1;
        ttab.SetToType("ATN");
        ttab.Translate(str1,str);
        atom.SetAtomicNum(atoi(str1.c_str()));
        ttab.SetToType("INT");
        ttab.Translate(str1,str);
        atom.SetType(str1);

        // stuff for optional fields

        buffer[109]='\0';
        sscanf(&buffer[101],"%lf", &charge);
        atom.SetPartialCharge(charge);
        mol.AddAtom(atom);
      }

    for (i = 1; i <= natoms; i++)
      for (j = 0; j < (signed)connections[i].size(); j++)
        mol.AddBond(i, connections[i][j].first, connections[i][j].second);

    mol.EndModify();

    OBBond *bond;
    vector<OBBond*>::iterator bi;
    for (bond = mol.BeginBond(bi);bond;bond = mol.NextBond(bi))
      if (bond->GetBO() == 5 && !bond->IsInRing())
        bond->SetBO(1);

    if ( natoms != (signed)mol.NumAtoms() )
      return(false);

    // clean out remaining blank lines
    while(ifs.peek() != EOF && ifs.good() &&
          (ifs.peek() == '\n' || ifs.peek() == '\r'))
      ifs.getline(buffer,BUFF_SIZE);

    return(true);
  }

  bool OBChemTsfm::Apply(OBMol &mol)
  {
    if (!_bgn.Match(mol))
      return(false);

    vector<vector<int> > mlist = _bgn.GetUMapList();

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

    if (!_vchrg.empty()) //modify charges
      {
        vector<vector<int> >::iterator i;
        vector<pair<int,int> >::iterator j;

        for (i = mlist.begin();i != mlist.end();++i)
          for (j = _vchrg.begin();j != _vchrg.end();++j)
            if (j->first < (signed)i->size()) //goof proofing
              mol.GetAtom((*i)[j->first])->SetFormalCharge(j->second);

        mol.UnsetImplicitValencePerceived();
      }

    if (!_vbond.empty()) //modify bond orders
      {
        OBBond *bond;
        vector<vector<int> >::iterator i;
        vector<pair<pair<int,int>,int> >::iterator j;
        for (i = mlist.begin();i != mlist.end();++i)
          for (j = _vbond.begin();j != _vbond.end();++j)
            {
              bond = mol.GetBond((*i)[j->first.first],(*i)[j->first.second]);
              if (!bond)
                {
                  obErrorLog.ThrowError(__FUNCTION__, "unable to find bond", obDebug);
                  continue;
                }

              bond->SetBO(j->second);
            }
      }

    if (!_vadel.empty() || !_vele.empty()) //delete atoms and change elements
      {
        vector<int>::iterator j;
        vector<vector<int> >::iterator i;

        if (!_vele.empty())
          {
            vector<pair<int,int> >::iterator k;
            for (i = mlist.begin();i != mlist.end();++i)
              for (k = _vele.begin();k != _vele.end();++k)
                mol.GetAtom((*i)[k->first])->SetAtomicNum(k->second);
          }

        //make sure same atom isn't deleted twice
        vector<bool> vda;
        vector<OBAtom*> vdel;
        vda.resize(mol.NumAtoms()+1,false);
        for (i = mlist.begin();i != mlist.end();++i)
          for (j = _vadel.begin();j != _vadel.end();++j)
            if (!vda[(*i)[*j]])
              {
                vda[(*i)[*j]] = true;
                vdel.push_back(mol.GetAtom((*i)[*j]));
              }

        vector<OBAtom*>::iterator k;
        for (k = vdel.begin();k != vdel.end();++k)
          mol.DeleteAtom((OBAtom*)*k);
      }

    return(true);
  }