C++ OBMol::BeginModify方法代码示例

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 ReadHIN(istream &ifs,OBMol &mol, const char *title)
{ 
  // Right now only read in the first molecule
  int i;
  int max, bo;
  char buffer[BUFF_SIZE];
  string str,str1;
  double x,y,z;
  OBAtom *atom;
  vector<string> vs;

  ifs.getline(buffer, BUFF_SIZE);
  while (strstr(buffer,"mol") == NULL)
    ifs.getline(buffer, BUFF_SIZE);
  ifs.getline(buffer, BUFF_SIZE);
  
  mol.BeginModify();
  while (strstr(buffer,"endmol") == NULL)
    {
      tokenize(vs,buffer); // Don't really know how long it'll be
      if (vs.size() < 11) break;
      atom = mol.NewAtom();
      atom->SetAtomicNum(etab.GetAtomicNum(vs[3].c_str()));
      x = atof((char*)vs[7].c_str());
      y = atof((char*)vs[8].c_str());
      z = atof((char*)vs[9].c_str());
      atom->SetVector(x,y,z);
      
      max = 11 + 2 * atoi((char *)vs[10].c_str());
      for (i = 11; i < max; i+=2)
	{
	  switch(((char*)vs[i+1].c_str())[0]) // First char in next token
	    {
	    case 's': bo = 1; break;
	    case 'd': bo = 2; break;
	    case 't': bo = 3; break;
	    case 'a': bo = 5; break;
	    default : bo = 1; break;
	    }
	  mol.AddBond(mol.NumAtoms(), atoi((char *)vs[i].c_str()), bo);
	}
      ifs.getline(buffer, BUFF_SIZE);
    }
  mol.EndModify();

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

bool XXXFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
  OBMol* pmol = pOb->CastAndClear<OBMol>();
  if(pmol==NULL)
      return false;

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

  pmol->BeginModify();

	/** Parse the input stream and use the OpenBabel API to populate the OBMol **/

	// To use an input option
	if(pConv->IsOption("s",OBConversion::INOPTIONS))
	{
		//Code for when -as is specified
	}

	/* If the molecule has other than 3D coordinates for its atoms, it
	is necessary to set the dimension to 0, or 2 */
	int dim;
	pmol->SetDimension(dim);

	pmol->EndModify();

	/* For multi-molecule formats, leave the input stream at the start of the
	   next molecule, ready for this routine to be called again.

	/* Return true if ok. Returning false means discard the OBMol and stop
	   converting, unless the -e option is set. With a multi-molecule inputstream
	   this will skip the current molecule and continue with the next, if SkipObjects()
	   has been defined. If it has not, and continuation after errors is still required,
	   it is necessary to leave the input stream at the beginning of next object when
	   returning false;*/
	return true;
}

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

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

    const char* title = pConv->GetTitle();
    char buffer[BUFF_SIZE];

    stringstream errorMsg;

    if (!ifs)
      return false; // We are attempting to read past the end of the file

    pmol->SetTitle(title);

    while (ifs.good() && ifs.getline(buffer,BUFF_SIZE)) {
      if (buffer[0] == '#')
        continue; // comment line
      if (EQn(buffer, "object", 6))
        break;
    }
    if (!ifs)
      return false; // ran out of lines

    vector<string> vs;
    tokenize(vs, buffer);

    // Number of grid points (voxels)
    vector<int> voxels(3);
    if (!EQn(buffer, "object", 6) || vs.size() != 8)
      return false;
    else {
      voxels[0] = atoi(vs[5].c_str());
      voxels[1] = atoi(vs[6].c_str());
      voxels[2] = atoi(vs[7].c_str());
    }

    double x, y, z;
    if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "origin", 6))
      return false;
    else {
      tokenize(vs, buffer);
      if (vs.size() != 4)
        return false;
      x = atof(vs[1].c_str());
      y = atof(vs[2].c_str());
      z = atof(vs[3].c_str());
    }
    vector3 origin(x, y, z);

    // now three lines with the x, y, and z axes
    vector<vector3> axes;
    for (unsigned int i = 0; i < 3; ++i) {
      if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "delta", 5))
        return false;
      else {
        tokenize(vs, buffer);
        if (vs.size() != 4)
          return false;
        x = atof(vs[1].c_str());
        y = atof(vs[2].c_str());
        z = atof(vs[3].c_str());
        axes.push_back(vector3(x, y, z));
      }
    }

    // Two remaining header lines before the data:
    /*
      object 2 class gridconnections counts nx ny nz
      object 3 class array type double rank 0 times n data follows
    */
    if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "object", 6))
      return false;
    if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "object", 6))
      return false;

    pmol->BeginModify();
    pmol->SetDimension(3);

    OBGridData *gd = new OBGridData;
    gd->SetAttribute("OpenDX");

    // get all values as one vector<double>
    char *endptr;
    vector<double> values;
    int n = voxels[0]*voxels[1]*voxels[2];
    int line = 0;
    values.reserve(n);
    while (ifs.getline(buffer, BUFF_SIZE))
    {
      ++line;
      if (EQn(buffer, "attribute", 9))
        break; // we're finished with reading data -- although we should probably have a voxel check in here too

      tokenize(vs, buffer);
      if (vs.size() == 0)
//.........这里部分代码省略.........

  bool OBChemTsfm::Apply(OBMol &mol)
  {
    if (!_bgn.Match(mol))
      return(false);
    mol.BeginModify();
    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
              OBAtom *atom = mol.GetAtom((*i)[j->first]);
              int old_charge = atom->GetFormalCharge();
              atom->SetFormalCharge(j->second);
              int new_hcount = atom->GetImplicitHCount() + (j->second - old_charge);
              if (new_hcount < 0)
                new_hcount = 0;
              atom->SetImplicitHCount(new_hcount);
            }
      }

    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;
                }
              unsigned int old_bond_order = bond->GetBondOrder();
              bond->SetBondOrder(j->second);
              for (int k = 0; k < 2; ++k) {
                OBAtom* atom = k == 0 ? bond->GetBeginAtom() : bond->GetEndAtom();
                int new_hcount = atom->GetImplicitHCount() - (j->second - old_bond_order);
                if (new_hcount < 0)
                  new_hcount = 0;
                atom->SetImplicitHCount(new_hcount);
              }
            }
      }

    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);
      }

    mol.EndModify();
    return(true);
  }

  bool ACRFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
  {
    OBMol* pmol = pOb->CastAndClear<OBMol>();
    if(pmol==NULL)
      return false;

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

    pmol->BeginModify();

    /** Parse the input stream and use the OpenBabel API to populate the OBMol **/
    int id;
    char buf[BUFF_SIZE];
    int atoms, bonds, tmp;
    float scale, dtmp;
    bool atom_input = false, bond_input = false;
    string type;
    //int from, to;
    double X,Y,Z;
    vector<string> vs;

    // read in one at a time
    /* WARNING: Atom id starts from zero in Carine; not so in openbabel.
     * Solution: increment atom id's */

    while (true) {
      ifs.getline(buf, BUFF_SIZE);
      if (ifs.eof()) {
        break;
      }

      if (sscanf(buf, "General Scale=%f\n", &dtmp)) {
        scale = dtmp;
        continue;
      } else if (sscanf(buf, "Number of Atoms in Crystal=%d\n", &tmp)) {
        atoms = tmp;
        atom_input = true;

        // read table column names
        ifs.getline(buf, BUFF_SIZE);
        continue;
      } else if (sscanf(buf, "Number of Links in Crystal=%d\n", &tmp)) {
        atom_input = false;
        bond_input = true;
        bonds = tmp;

        // read table column names
        ifs.getline(buf, BUFF_SIZE);
        continue;
      } else if ( '#' == buf[0] || '\r' == buf[0] || '\n' == buf[0] ) {
        // between sections, in both windows and unix.
        continue;
      }
      tokenize(vs, buf, " \t\r\n");

      if (atom_input) {
	if (vs.size() < 9) return false; // timvdm 18/06/2008
        id = atoi((char*)vs[0].c_str()) + 1; // see warning above
        type = vs[1];
        X = atof((char*)vs[6].c_str())/scale;
        Y = atof((char*)vs[7].c_str())/scale;
        Z = atof((char*)vs[8].c_str())/scale;

        OBAtom* a = pmol->NewAtom();
        if (*(type.c_str()) != '*')
          a->SetAtomicNum(etab.GetAtomicNum(type.c_str()));
        a->SetVector(X,Y,Z);

      } else if (bond_input) {
	if (vs.size() < 2) return false; // timvdm 18/06/2008
        // add to pmol
        if (!pmol->AddBond(atoi((char*)vs[0].c_str()) + 1, atoi((char*)vs[1].c_str()) + 1,
                           1 /* bond order not specified in Carine, use PerceiveBondOrder later */))
          {
            obErrorLog.ThrowError(__FUNCTION__, "addition of bond between " + vs[0] + " and " + vs[1] + " failed", obError);
            return false;
          }
      }
    }

    /* got sanity? */
    if ( pmol->NumBonds() != bonds ) {
      // then we read a different number of bonds than those promised.
      obErrorLog.ThrowError(__FUNCTION__, "Number of bonds read does not match the number promised", obError);
      return false;
    } else if ( pmol->NumAtoms() != atoms ) {
      obErrorLog.ThrowError(__FUNCTION__, "Number of atoms read does not match the number promised", obError);
      return false;
    }

    pmol->PerceiveBondOrders();

    pmol->EndModify();

    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);
}

bool GAMESSUKFormat::ReadGeometry(OBMol &mol, vector<string> &geomList)
{
	
	/* Read a geometry from a list. Any variables that appear in the geometry need
	 * to be in the variables map that should have been populated before this is called.
	 */
	
	if (geomList.size()==0){
		obErrorLog.ThrowError(__FUNCTION__, 
				"Problems reading a GAMESS-UK Input file: ReadGeometry got empty list",
				obWarning);
		return false;
	}

	vector<string> tokens; // list of lines and list of tokens on a line
	string line; // For convenience so we can refer to lines from the iterator as 'line'
	double factor=BOHR_TO_ANGSTROM; // The coordinate conversion factor for handling bohr/angstrom issues

	mol.BeginModify();	
	// Clear out any existing information
	mol.Clear();
	vic.clear();
	
	ReadMode=SKIP;
	bool ContainsZmatrix=false;
	int zmatLineCount=0;

	/*	
	cerr << "ReadGeometry got geometry list: \n";
	for (vector<string>::iterator i=geomList.begin(); i !=geomList.end(); i++) {
		
		// Alias the line
		line = *i; 
		cerr << "line: " << line << endl;
	}
	*/
	
	for (vector<string>::iterator i=geomList.begin(); i !=geomList.end(); i++) {
		
		// Alias the line
		line = *i; 
		
		//cerr << "ReadGeometry line is: " << line << endl;

		// Check for commas & split with that as the separator if necessary
		if (line.find(',')!=string::npos) {
			tokenize(tokens, line, ",");
		} else {
			tokenize(tokens, line, " \t\n");
		}


		// Set the mode
		if (line.compare(0, 4, "zmat")==0 || line.compare(0, 4, "inte")==0) {
			ReadMode=ZMATRIX;
			//cout << "ZMATRIX mode " << ReadMode << endl;
			//cout << "tokens.size()" << tokens.size() << endl;
			if (tokens.size()>1) if (IsUnits(tokens[1])) factor=Rescale(tokens[1]);
			ContainsZmatrix=true;
			vic.push_back((OBInternalCoord*)NULL); // OBMol indexed from 1 -- potential atom index problem
		} else if (line.compare(0, 4, "coor")==0 || line.compare(0, 4, "cart")==0 ||line.compare(0, 4, "geom")==0) {
			ReadMode=CARTESIAN;
			//cout << "CARTESIAN mode " << ReadMode << endl;
			if (tokens.size()>1) if (IsUnits(tokens[1])) factor=Rescale(tokens[1]);
			
		/*
		 We need to have read the variables first
		} else if (line.compare(0, 4, "vari")==0) {
			ReadMode=VARIABLES;
			//cout << "VARIABLES mode "<< ReadMode << endl;
			if (tokens.size() == 2) factor=Rescale(tokens[1]);
			//cout << "Factor now " << factor << endl;
		} else if (line.compare(0, 4, "cons")==0) {
			ReadMode=CONSTANTS;
			//cout << "CONSTANTS mode\n";
			if (tokens.size() == 2)
				factor=Rescale(tokens[1]);
			//cout << "Factor now " << factor << endl;
	    */
			
		} else if (line.compare(0, 3, "end")==0) {
			ReadMode=SKIP;
			//cout << "SKIP mode " << ReadMode << endl;
		} else {
			if (ReadMode==SKIP) continue;
			if (ReadMode==ZMATRIX) {
				// Create an atom
				OBAtom *atom = mol.NewAtom();
				// Read the ZMatrix definition line
				if (! ReadLineZmatrix(mol,atom,tokens,factor,&zmatLineCount) )
				{
					errorMsg << "Problems reading a GAMESS-UK Input file: "
							<< "Could not read zmat line: " << line;
					obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() ,
							obWarning);
					return (false);
				}	
				
			} // End ReadMode ZMATRIX

//.........这里部分代码省略.........

  bool PWscfFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
  {
    OBMol* pmol = pOb->CastAndClear<OBMol>();
    if(pmol==NULL)
      return false;

    //Define some references so we can use the old parameter names
    istream &ifs = *pConv->GetInStream();

    char buffer[BUFF_SIZE], tag[BUFF_SIZE];
    double x,y,z;
    double alat = 1.0;
    vector<string> vs;
    matrix3x3 ortho;
    int atomicNum;
    OBUnitCell *cell = new OBUnitCell();
    bool hasEnthalpy=false;
    double enthalpy, pv;

    pmol->BeginModify();

    while (ifs.getline(buffer,BUFF_SIZE)) {

      // Older version of pwscf may use this for alat
      if (strstr(buffer, "lattice parameter (a_0)")) {
        tokenize(vs, buffer);
        alat = atof(vs.at(4).c_str());
      }

      // Newer versions will use this for alat instead
      if (strstr(buffer, "lattice parameter (alat)")) {
        tokenize(vs, buffer);
        alat = atof(vs.at(4).c_str());
      }

      // Unit cell info
      // Newer versions will also say "CELL_PARAMETERS" to complain that no
      // units were specified
      if (strstr(buffer, "CELL_PARAMETERS") &&
          !strstr(buffer, "no units specified in CELL_PARAMETERS card")) {
        // Discover units
        double conv = 1.0;
        tokenize(vs, buffer);

        if (strstr(vs[1].c_str(), "alat")) {
          conv = alat * BOHR_TO_ANGSTROM;
        }
        else if (strstr(vs[1].c_str(), "bohr")) {
          conv = BOHR_TO_ANGSTROM;
        }
        // Add others if needed

        double v11, v12, v13,
          v21, v22, v23,
          v31, v32, v33;

        ifs.getline(buffer,BUFF_SIZE); // v1
        tokenize(vs, buffer);
        v11 = atof(vs.at(0).c_str()) * conv;
        v12 = atof(vs.at(1).c_str()) * conv;
        v13 = atof(vs.at(2).c_str()) * conv;

        ifs.getline(buffer,BUFF_SIZE); // v2
        tokenize(vs, buffer);
        v21 = atof(vs.at(0).c_str()) * conv;
        v22 = atof(vs.at(1).c_str()) * conv;
        v23 = atof(vs.at(2).c_str()) * conv;

        ifs.getline(buffer,BUFF_SIZE); // v3
        tokenize(vs, buffer);
        v31 = atof(vs.at(0).c_str()) * conv;
        v32 = atof(vs.at(1).c_str()) * conv;
        v33 = atof(vs.at(2).c_str()) * conv;

        // Build unit cell
        cell->SetData(vector3(v11,v12,v13),
                      vector3(v21,v22,v23),
                      vector3(v31,v32,v33));
      }

      // Unit cell info (for non-variable cell calcs)
      if (strstr(buffer, "crystal axes: (cart. coord. in units of a_0)") ||
          strstr(buffer, "crystal axes: (cart. coord. in units of alat)")) {
        double conv = alat * BOHR_TO_ANGSTROM;
        double v11, v12, v13,
          v21, v22, v23,
          v31, v32, v33;

        ifs.getline(buffer,BUFF_SIZE); // v1
        tokenize(vs, buffer);
        v11 = atof(vs.at(3).c_str()) * conv;
        v12 = atof(vs.at(4).c_str()) * conv;
        v13 = atof(vs.at(5).c_str()) * conv;

        ifs.getline(buffer,BUFF_SIZE); // v2
        tokenize(vs, buffer);
        v21 = atof(vs.at(3).c_str()) * conv;
        v22 = atof(vs.at(4).c_str()) * conv;
        v23 = atof(vs.at(5).c_str()) * conv;

//.........这里部分代码省略.........

int mol(int argc, char* argv[])
{
  int defaultchoice = 1;
  
  int choice = defaultchoice;

  if (argc > 1) {
    if(sscanf(argv[1], "%d", &choice) != 1) {
      printf("Couldn't parse that input as a number\n");
      return -1;
    }
  }


  // Define location of file formats for testing
  #ifdef FORMATDIR
    char env[BUFF_SIZE];
    snprintf(env, BUFF_SIZE, "BABEL_LIBDIR=%s", FORMATDIR);
    putenv(env);
  #endif

  cout << "# Unit tests for OBMol \n";

  cout << "ok 1\n"; // for loading tests

  OBMol emptyMol, testMol1;
  cout << "ok 2\n"; // ctor works

  testMol1.ReserveAtoms(-1);
  testMol1.ReserveAtoms(0);
  testMol1.ReserveAtoms(2);
  cout << "ok 3\n";

  // atom component tests

  if (testMol1.NumAtoms() == 0) {
    cout << "ok 4\n";
  } else {
    cout << "not ok 4\n";
  }

  testMol1.NewAtom();
  if (testMol1.NumAtoms() == 1) {
    cout << "ok 5\n";
  } else {
    cout << "not ok 5\n";
  }

  testMol1.NewAtom();
  testMol1.AddBond(1, 2, 1);
  if (testMol1.NumBonds() == 1) {
    cout << "ok 6\n";
  } else {
    cout << "not ok 6\n";
  }

  testMol1.Clear();
  if (testMol1.NumAtoms() == 0) {
    cout << "ok 7\n";
  } else {
    cout << "not ok 7\n";
  }

  ifstream ifs1(kd3file.c_str());
  if (!ifs1)
    {
      cout << "Bail out! Cannot read input file!" << endl;
      return(-1);
    }
  OBConversion conv(&ifs1, &cout);
  OBFormat* pFormat;
  
  pFormat = conv.FindFormat("XYZ");
  if ( pFormat == NULL )
    {
      cout << "Bail out! Cannot read file format!" << endl;
      return(-1);
    }
  if (! conv.SetInAndOutFormats(pFormat, pFormat))
    {
      cout << "Bail out! File format isn't loaded" << endl;
      return (-1);
    }

  OBMol testMol2D, testMol3D;
  if (conv.Read(&testMol3D))
    cout << "ok 8\n";
  else
    cout << "not ok 8\n";
  testMol3D.Center();
  
  // test bond insertion (PR#1665649)
  OBMol doubleBondMol;
  OBAtom *a1, *a2;
  OBBond *b;
  doubleBondMol.BeginModify();
  a1 = doubleBondMol.NewAtom();
  a1->SetVector(0.0, 0.0, 0.0);
  a1->SetAtomicNum(6);
  a2 = doubleBondMol.NewAtom();
//.........这里部分代码省略.........