C++ OBMol::SetDimension方法代码示例

bool OpGen2D::Do(OBBase* pOb, OpMap* pmap, const char* OptionText)
{
  OBMol* pmol = dynamic_cast<OBMol*>(pOb);
  if(!pmol)
    return false;

  generateDiagram(pmol);
  pmol->SetDimension(2);

  return true;
}

//------------------------------------------------------------------------------
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;
}

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 ThermoFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv)
{
  OBMol* pmol = pOb->CastAndClear<OBMol>();
  if(!pmol)
    return false;
  bool stopOnEnd = pConv->IsOption("e",OBConversion::INOPTIONS)!=NULL;
  pmol->SetDimension(0);
  OBNasaThermoData* pND = new OBNasaThermoData; //to store rate constant data
  pND->SetOrigin(fileformatInput);
  pmol->SetData(pND);

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

  double DefaultMidT = 1500;
  char ln[BUFF_SIZE];
  unsigned int i;

  //find line with 1 in col 80
  do
  {
    if(!ifs.getline(ln,BUFF_SIZE) || stopOnEnd && !strncasecmp(ln,"END",3))
      return false;
  }while(ln[79]!='1');

  char phase, nam[25], dum[7], elname[3];
  elname[2]=0;
  int elnum;
  double Coeff[14];

  sscanf(ln,"%18s%6s",nam,dum);
  pmol->SetTitle(nam);
  char* p=ln+24;
  if(ln[80]=='&')
  {
    //Reaction Design extension
    p+=20;
    string line;
    if(!getline(ifs,line))return false;
    vector<string> toks;
    tokenize(toks,line," \t\n\r");
    for(i=0;i<toks.size();i+=2)
    {
      OBAtom atom;
      atom.SetAtomicNum(etab.GetAtomicNum(toks[i].c_str()));
      elnum = atoi(toks[i+1].c_str());
      atom.ForceNoH();
      for(;elnum>0;--elnum)
        pmol->AddAtom(atom);
    }
  }
  else
  {
    for(i=0;i<4;i++,p+=5)
    {
      char snum[4]={0,0,0,0};//Was problem with F   10   0 reading as ten
      sscanf(p,"%c%c%c%c%c",elname,elname+1,snum,snum+1,snum+2);
      elnum=atoi(snum);
      if(elname[0]!=' ' && elname[0]!='0')
      {
        if(elname[1]==' ')
          elname[1]=0;
        OBAtom atom;
        atom.SetAtomicNum(etab.GetAtomicNum(elname));
        atom.ForceNoH();
        for(;elnum>0;--elnum)
          pmol->AddAtom(atom);
      }
    }
  }
  double LoT, HiT, MidT=0;
  /* int nc = */sscanf(p,"%c%10lf%10lf10%lf",&phase, &LoT, &HiT, &MidT);
  pND->SetPhase(phase);
  pND->SetLoT(LoT);
  pND->SetHiT(HiT);
  if(MidT>HiT || MidT<LoT)
    MidT=DefaultMidT;
  pND->SetMidT(MidT);
  if (!ifs.getline(ln, BUFF_SIZE)) return false;
  p=ln;
  for(i=0;i<5;i++,p+=15)
    sscanf(p,"%15lf",&Coeff[i]);
  if (!ifs.getline(ln, BUFF_SIZE)) return false;
  p=ln;
  for(i=5;i<10;i++,p+=15)
    sscanf(p,"%15lf",&Coeff[i]);
  if (!ifs.getline(ln, BUFF_SIZE)) return false;
  p=ln;
  for(i=10;i<14;i++,p+=15)
    sscanf(p,"%15lf",&Coeff[i]);

  for(i=0;i<14;++i)
    pND->SetCoeff(i, Coeff[i]);

  pmol->AssignSpinMultiplicity();
  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.........