C++ OBMol::ConnectTheDots方法代码示例

//------------------------------------------------------------------------------
bool OBMoldenFormat::ReadMolecule( OBBase* pOb, OBConversion* pConv )
{
    OBMol* pmol = dynamic_cast< OBMol* >(pOb);
    if( pmol == 0 ) return false;

    istream& ifs = *pConv->GetInStream();

    pmol->BeginModify();
    pmol->SetDimension( 3 );
    string lineBuffer;
    getline( ifs, lineBuffer );

    while( ifs && lineBuffer.find( "[Atoms]" ) == string::npos 
    	   && lineBuffer.find( "[ATOMS]" ) == string::npos )
    {
        getline( ifs, lineBuffer );
    }

    if( !ifs ) return false;

    //[Atoms] AU OR Angs
    double factor = 1.; // Angstrom
    if( lineBuffer.find( "AU" ) != string::npos ) factor = 0.529177249; // Bohr

    while( ifs )
    {
        getline( ifs, lineBuffer );
        if( lineBuffer.size() == 0 ) continue;
        if( lineBuffer.find( '[' ) != string::npos ) break;
        istringstream is( lineBuffer );
        string atomName;
        int atomId;
        int atomicNumber;
        double x, y, z;
        is >> atomName >> atomId >> atomicNumber >> x >> y >> z;
        OBAtom* atom = pmol->NewAtom();
        if( !atom ) break;
        atom->SetAtomicNum( atomicNumber );
        atom->SetVector( x * factor, y * factor, z * factor );
    }

    if( !pConv->IsOption( "b", OBConversion::INOPTIONS ) ) pmol->ConnectTheDots();
    if (!pConv->IsOption( "s", OBConversion::INOPTIONS )
        && !pConv->IsOption( "b", OBConversion::INOPTIONS ) )
    {
        pmol->PerceiveBondOrders();
    }
    pmol->EndModify();

    return true;
}

  int ReadPQS_geom(istream &ifs, OBMol &mol, const char *title,
                   int input_style, double bohr_to_angstrom)
  {
    int atom_count=0;
    double x, y, z;
    char buffer[BUFF_SIZE];
    string str;
    OBAtom *atom;
    vector<string> vs;

    mol.Clear();
    mol.BeginModify();

    while (ifs.getline(buffer,BUFF_SIZE) && !card_found(buffer))
      {
        if (buffer[0]!='$')
          {
            tokenize(vs, buffer);
            if (vs.size() < 1) return false; // timvdm 18/06/2008
            atom=mol.NewAtom();
            str=vs[0];
            if (input_style==0)
              {
                if (vs.size() < 4) return false; // timvdm 18/06/2008
                atom->SetAtomicNum(OBElements::GetAtomicNum(str.c_str()));
                x=atof((char*) vs[1].c_str())*bohr_to_angstrom;
                y=atof((char*) vs[2].c_str())*bohr_to_angstrom;
                z=atof((char*) vs[3].c_str())*bohr_to_angstrom;
              }
            else
              {
                if (vs.size() < 5) return false; // timvdm 18/06/2008
                str.replace (0,2,"");
                atom->SetAtomicNum(OBElements::GetAtomicNum(str.c_str()));
                x=atof((char*) vs[2].c_str())*bohr_to_angstrom;
                y=atof((char*) vs[3].c_str())*bohr_to_angstrom;
                z=atof((char*) vs[4].c_str())*bohr_to_angstrom;
              }
            atom->SetVector(x, y, z);
            atom_count++;
          }
      }

    mol.ConnectTheDots();
    mol.PerceiveBondOrders();

    mol.EndModify();
    mol.SetTitle(title);

    return atom_count;
  }

bool ReadBiosymCAR(istream &ifs,OBMol &mol, const char *title)
{
  char buffer[BUFF_SIZE];
  string str;
  double x,y,z;
  OBAtom *atom;
  vector<string> vs;

  mol.BeginModify();

  while	(ifs.getline(buffer,BUFF_SIZE))
    {
      if(strstr(buffer,"PBC") != NULL)
	{
	  if(strstr(buffer,"ON") != NULL)
	    {
	      ifs.getline(buffer,BUFF_SIZE);
	      ifs.getline(buffer,BUFF_SIZE);
	      ifs.getline(buffer,BUFF_SIZE);
	    }
	  else
	    {
	      ifs.getline(buffer,BUFF_SIZE);
	      ifs.getline(buffer,BUFF_SIZE);
	    }
	  break;
	}
    }

  while	(ifs.getline(buffer,BUFF_SIZE))
    {
      if(strstr(buffer,"end") != NULL)
	break;

      atom = mol.NewAtom();

      tokenize(vs,buffer);
      atom->SetAtomicNum(etab.GetAtomicNum(vs[7].c_str()));
      x = atof((char*)vs[1].c_str());
      y = atof((char*)vs[2].c_str());
      z = atof((char*)vs[3].c_str());
      atom->SetVector(x,y,z);
    }
  mol.EndModify();

  mol.ConnectTheDots();
  mol.PerceiveBondOrders();
  mol.SetTitle(title);
  return(true);
}

bool ReadViewMol(istream &ifs,OBMol &mol,const char *title)
{
  char buffer[BUFF_SIZE];
  OBAtom *atom;
  double x,y,z, border;
  double factor = 1.0;
  int bgn, end, order;
  vector<string> vs;
  bool foundTitle = false;
  bool foundBonds = false;

  mol.BeginModify();

  while	(ifs.getline(buffer,BUFF_SIZE))
    {
      if (strstr(buffer,"$title") != NULL)
	{
	  if (!ifs.getline(buffer,BUFF_SIZE)) return (false);
	  mol.SetTitle(buffer);
	  foundTitle = true;
	}
      else if (strstr(buffer,"$coord") != NULL)
	{
	  tokenize(vs,buffer);
	  if (vs.size() == 2)
	    factor = atof((char*)vs[1].c_str()); // conversion to angstrom
	  while (ifs.getline(buffer,BUFF_SIZE))
	    {
	      if (buffer[0] == '$') break;
	      tokenize(vs,buffer);
	      if (vs.size() != 4) return(false);
	      atom = mol.NewAtom();
	      x = atof((char*)vs[0].c_str()) * factor;
	      y = atof((char*)vs[1].c_str()) * factor;
	      z = atof((char*)vs[2].c_str()) * factor;
	      atom->SetVector(x,y,z); //set coordinates
	      atom->SetAtomicNum(etab.GetAtomicNum(vs[3].c_str()));
	    }
	}
      else if (strstr(buffer,"$bonds") != NULL) 
	{
	  foundBonds = true;
	  while (ifs.getline(buffer,BUFF_SIZE))
	    {
	      if (buffer[0] == '$') break;
	      sscanf(buffer,"%d %d %lf",&bgn,&end, &border);
	      if (border > 1.0)
		order = int(border);
	      else
		order = 1;
	      mol.AddBond(bgn+1,end+1,order);
	    }
	}
      else if (strstr(buffer,"$end") != NULL)
	break;
    } // while
  
  mol.EndModify();

  if (!foundTitle)
    mol.SetTitle(title);
  if (!foundBonds)
    {
      mol.ConnectTheDots();
      mol.PerceiveBondOrders();
    }
  return(true);
}

//.........这里部分代码省略.........
    cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	 << "  Problems reading the first line. The first line must contain the number of atoms." << endl
	 << "  OpenBabel found the line '" << buffer << "'" << endl
	 << "  which could not be interpreted as a number." << endl;
    return(false);
  }
  if (!natoms) {
    cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	 << "  Problems reading the first line. The first line must contain the number of atoms." << endl
	 << "  OpenBabel found the number '0' which obviously does not work." << endl;
    return(false);
  }
  mol.ReserveAtoms(natoms);
  
  // The next line contains a title string for the molecule. Use this
  // as the title for the molecule if the line is not
  // empty. Otherwise, use the title given by the calling function.
  if (!ifs.getline(buffer,BUFF_SIZE)) {
    cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	 << "  Could not read the second line, file error." << endl;
    return(false);
  }
  if (strlen(buffer) == 0)
    mol.SetTitle(buffer);
  else
    mol.SetTitle(title);
  
  // The next lines contain four items each, separated by white
  // spaces: the atom type, and the coordinates of the atom
  vector<string> vs;
  for (unsigned int i = 1; i <= natoms; i ++) {
    if (!ifs.getline(buffer,BUFF_SIZE)) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << ", file error." << endl
	   << "  According to line one, there should be " << natoms << " atoms, and therefore " << natoms+2 << " lines in the file" << endl;
      return(false);
    }
    tokenize(vs,buffer);
    if (vs.size() != 4) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << "." << endl
	   << "  OpenBabel found the line '" << buffer << "'" << endl
	   << "  According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
	   << "  However, OpenBabel found " << vs.size() << " items." << endl;
      return(false);
    }
    
    // Atom Type: get the atomic number from the element table, using
    // the first entry in the currently read line. If the entry makes
    // sense, set the atomic number and leave the atomic type open
    // (the type is then later faulted in when atom->GetType() is
    // called). If the entry does not make sense to use, set the atom
    // type manually, assuming that the author of the xyz-file had
    // something "special" in mind.
    OBAtom *atom  = mol.NewAtom();
    int atomicNum = etab.GetAtomicNum(vs[0].c_str());
    atom->SetAtomicNum(etab.GetAtomicNum(vs[0].c_str())); //set atomic number, or '0' if the atom type is not recognized
    if (atomicNum == 0)
      atom->SetType(vs[0]);

    // Read the atom coordinates
    char *endptr;
    double x = strtod((char*)vs[1].c_str(),&endptr);
    if (endptr == (char*)vs[1].c_str()) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << "." << endl
	   << "  OpenBabel found the line '" << buffer << "'" << endl
	   << "  According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
	   << "  Item #0: Atom Type, Items #1-#3 cartesian coordinates in Angstrom." << endl
	   << "  OpenBabel could not interpret item #1 as a number." << endl;
      return(false);
    }
    double y = strtod((char*)vs[2].c_str(),&endptr);
    if (endptr == (char*)vs[2].c_str()) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << "." << endl
	   << "  OpenBabel found the line '" << buffer << "'" << endl
	   << "  According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
	   << "  Item #0: Atom Type, Items #1-#3 cartesian coordinates in Angstrom." << endl
	   << "  OpenBabel could not interpret item #2 as a number." << endl;
      return(false);
    }
    double z = strtod((char*)vs[3].c_str(),&endptr);
    if (endptr == (char*)vs[3].c_str()) {
      cerr << "WARNING: Problems reading an XYZ file, method 'bool ReadXYZ(istream &,OBMol &,const char *)'" << endl
	   << "  Could not read line #" << i+2 << "." << endl
	   << "  OpenBabel found the line '" << buffer << "'" << endl
	   << "  According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl
	   << "  Item #0: Atom Type, Items #1-#3 cartesian coordinates in Angstrom." << endl
	   << "  OpenBabel could not interpret item #3 as a number." << endl;
      return(false);
    }
    atom->SetVector(x,y,z); //set coordinates
  }

  mol.ConnectTheDots();
  mol.PerceiveBondOrders();
  
  return(true);
}