C++ OBAtom::SetAtomicNum方法代码示例

  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;
  }

/* FUNCTION: basicExportTest */
void OpenBabelImportExportTest::basicExportTest() {

	// Create a water molecule for frame 0
	//
	int frameSetId = entityManager->addFrameSet();
	int frameIndex = entityManager->addFrame(frameSetId);
	NXMoleculeSet* rootMoleculeSet =
		entityManager->getRootMoleculeSet(frameSetId, frameIndex);
	OBMol* molecule = rootMoleculeSet->newMolecule();
	OBAtom* atomO = molecule->NewAtom();
	atomO->SetAtomicNum(etab.GetAtomicNum("O")); // Oxygen
	atomO->SetVector(0.00000000, 0.00000000, 0.37000000); // Angstroms
	OBAtom* atomH1 = molecule->NewAtom();
	atomH1->SetAtomicNum(etab.GetAtomicNum("H")); // Hydrogen
	atomH1->SetVector(0.78000000, 0.00000000, -0.18000000);
	OBAtom* atomH2 = molecule->NewAtom();
	atomH2->SetAtomicNum(etab.GetAtomicNum("H")); // Hydrogen
	atomH2->SetVector(-0.78000000, 0.00000000, -0.18000000);
	OBBond* bond = molecule->NewBond();
	bond->SetBegin(atomO);
	bond->SetEnd(atomH1);
	bond = molecule->NewBond();
	bond->SetBegin(atomO);
	bond->SetEnd(atomH2);
	
	// Write it with the OpenBabelImportExport plugin
	NXCommandResult* commandResult =
		entityManager->exportToFile("testOpenBabel.pdb", frameSetId, -1);
	if (commandResult->getResult() != NX_CMD_SUCCESS)
		printf("\n%s\n", qPrintable(GetNV1ResultCodeString(commandResult)));
	CPPUNIT_ASSERT(commandResult->getResult() == NX_CMD_SUCCESS);
}

bool ReadFeat(istream &ifs,OBMol &mol, const char *title)
{
  char buffer[BUFF_SIZE];
  int i,natoms;

  ifs.getline(buffer,BUFF_SIZE);
  sscanf(buffer,"%d",&natoms);

  mol.ReserveAtoms(natoms);
  mol.BeginModify();

  if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
  mol.SetTitle(buffer);

  double x,y,z;
  char type[20];
  OBAtom *atom;
  for (i = 0; i < natoms;i++)
  {
    if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
    sscanf(buffer,"%s %lf %lf %lf",
	   type,
	   &x,
	   &y,
	   &z);
    CleanAtomType(type);
    atom = mol.NewAtom();
    atom->SetVector(x,y,z);
    atom->SetAtomicNum(etab.GetAtomicNum(type));
  }

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

bool PubChemFormat::EndElement(const string& name)
{
  unsigned int i;
	if(name=="PC-Atoms")
	{
		for(i=0;i<AtNum.size();++i)
		{
			OBAtom* pAtom = _pmol->NewAtom();
			pAtom->SetAtomicNum(AtNum[i]);
		}
	}
	else if(name=="PC-Bonds")
	{
		for(i=0;i<BondBeginAtIndx.size();++i)
			_pmol->AddBond(BondBeginAtIndx[i],BondEndAtIndx[i],BondOrder[i]);
	}
	else if(name=="PC-Conformer")
	{
		++ConformerIndx;
		if(Coordz.size()!=Coordx.size())
			Coordz.resize(Coordx.size());
		for(i=0;i<CoordIndx.size();++i)
		{
			OBAtom* pAtom = _pmol->GetAtom(CoordIndx[i]);
			pAtom->SetVector(Coordx[i],Coordy[i],Coordz[i]);
		}
	}
	else if(name=="PC-Compound") //this is the end of the molecule we are extracting
	{
		_pmol->EndModify();
		return false;//means stop parsing
	}
	return true;
}

 /**
 Method reads coordinates from input stream (ifs) and
 writes it into supplied OBMol object (molecule).
 Input stream must be set to begining of coordinates
 table in nwo file. (Line after "Output coordinates...")
 Stream will be set at next line after geometry table.
 If one of input arguments is NULL method returns without
 any changes
 If "molecule" already contain geometry - method will write
 new geometry as conformer.
 If "molecule" contain geometry which incompatible with read
 data method returns without changes.
 */
 void NWChemOutputFormat::ReadCoordinates(istream* ifs, OBMol* molecule)
 {
   if ((molecule == NULL) || (ifs == NULL))
       return;
   vector<string> vs;
   char buffer[BUFF_SIZE];
   double x, y, z;
   unsigned int natoms = molecule->NumAtoms();
   bool from_scratch = false;
   double* coordinates;
   if (natoms == 0)
       from_scratch = true;
   else
       coordinates = new double[3*natoms];
   ifs->getline(buffer,BUFF_SIZE);	// blank
   ifs->getline(buffer,BUFF_SIZE);	// column headings
   ifs->getline(buffer,BUFF_SIZE);	// ---- ----- ----
   ifs->getline(buffer,BUFF_SIZE);
   tokenize(vs,buffer);
   unsigned int i=0;
   while (vs.size() == 6)
   {
       x = atof((char*)vs[3].c_str());
       y = atof((char*)vs[4].c_str());
       z = atof((char*)vs[5].c_str());
       if (from_scratch)
       {
           // set atomic number
           OBAtom* atom = molecule->NewAtom();
           atom->SetAtomicNum(atoi(vs[2].c_str()));
           atom->SetVector(x,y,z);
       }
       else
       {
           // check atomic number
           if ((i>=natoms) || (molecule->GetAtom(i+1)->GetAtomicNum() != atoi(vs[2].c_str())))
           {
               delete[] coordinates;
               return;
           }
           coordinates[i*3] = x;
           coordinates[i*3+1] = y;
           coordinates[i*3+2] = z;
           i++;
       }
       if (!ifs->getline(buffer,BUFF_SIZE))
         break;
       tokenize(vs,buffer);
   }
   if (from_scratch) 
   {
       return;
   }
   if (i != natoms) {
       delete[] coordinates;
       return;
   }
   molecule->AddConformer(coordinates);
 }

  /**
  Method reads partial charges from input stream (ifs)
  and writes them to supplied OBMol object (molecule)
  Input stream must be set to begining of charges
  table in nwo file. (Line after "Mulliken analysis of the total density")
  Stream will be set at next line after charges table.
  If reading charges failed or "molecule" contains
  data incompatible with read charges then "molecule"
  wont be changed.
  */
  void NWChemOutputFormat::ReadPartialCharges(istream* ifs, OBMol* molecule)
  {
    if ((molecule == NULL) || (ifs == NULL))
        return;
    vector<string> vs;
    char buffer[BUFF_SIZE];
    bool from_scratch = false;
    vector<int> charges;
    vector<double> partial_charges;
    unsigned int natoms = molecule->NumAtoms();

    if (natoms == 0)
        from_scratch = true;
    ifs->getline(buffer,BUFF_SIZE); // ---- ----- ----
    ifs->getline(buffer,BUFF_SIZE);	// blank
    ifs->getline(buffer,BUFF_SIZE);	// column headings
    ifs->getline(buffer,BUFF_SIZE);	// ---- ----- ----
    ifs->getline(buffer,BUFF_SIZE);
    tokenize(vs, buffer);

    // N Symbol    Charge     PartialCharge+Charge   ShellCharges
    // 0   1          2                3                4,etc
    unsigned int i = 1;
    while (vs.size() >= 4)
    {
        int charge = atoi(vs[2].c_str());
        if (!from_scratch)
        {
            if (i > natoms)
                return;
            if (molecule->GetAtom(i++)->GetAtomicNum() != charge)
                return;
        }
        else
            charges.push_back(charge);
        partial_charges.push_back(atof(vs[3].c_str()) - charge);
        ifs->getline(buffer,BUFF_SIZE);
        tokenize(vs, buffer);
    }

    if (from_scratch)
        molecule->ReserveAtoms(partial_charges.size());
    else if (partial_charges.size() != natoms)
        return;
    for(unsigned int j=0;j<partial_charges.size();j++)
    {
        OBAtom* atom;
        if (from_scratch)
        {
            atom = molecule->NewAtom();
            atom->SetAtomicNum(charges[j]);
        }
        else
        {
            atom = molecule->GetAtom(j+1);
        }
        atom->SetPartialCharge(partial_charges[j]);
    }
  }

bool AmberPrepFormat::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();
    OBMol &mol = *pmol;
    const char* title = pConv->GetTitle();

    char buffer[BUFF_SIZE];
    string str,str1;
    OBAtom *atom;
    OBInternalCoord *coord;
    vector<string> vs;
    vector<OBInternalCoord*> internals;

    mol.BeginModify();

    while	(ifs.getline(buffer,BUFF_SIZE))
    {
        tokenize(vs,buffer);
        if (vs.size() == 10)
        {
            atom = mol.NewAtom();
            coord = new OBInternalCoord();
            if (mol.NumAtoms() > 1)
                coord->_a = mol.GetAtom(atoi(vs[4].c_str()));
            if (mol.NumAtoms() > 2)
                coord->_b = mol.GetAtom(atoi(vs[5].c_str()));
            if (mol.NumAtoms() > 3)
                coord->_c = mol.GetAtom(atoi(vs[6].c_str()));
            coord->_dst = atof(vs[7].c_str());
            coord->_ang = atof(vs[8].c_str());
            coord->_tor = atof(vs[9].c_str());
            internals.push_back(coord);

            atom->SetAtomicNum(etab.GetAtomicNum(vs[1].c_str()));

            if (!ifs.getline(buffer,BUFF_SIZE))
                break;
            tokenize(vs,buffer);
        }
    }

    if (internals.size() > 0)
      InternalToCartesian(internals,mol);

    if (!pConv->IsOption("b",OBConversion::INOPTIONS))
      mol.ConnectTheDots();
    if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS))
      mol.PerceiveBondOrders();

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

  bool BallStickFormat::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();
    OBMol &mol = *pmol;
    const char* title = pConv->GetTitle();

    int i,natoms;
    char buffer[BUFF_SIZE];

    if (!ifs.getline(buffer,BUFF_SIZE))
      return(false);
    if (!ifs.getline(buffer,BUFF_SIZE))
      return(false);
    sscanf(buffer,"%d",&natoms);
    mol.ReserveAtoms(natoms);
    mol.BeginModify();

    double x,y,z;
    OBAtom *atom;
    vector<string> vs;
    vector<string>::iterator j;

    for (i = 1; i <= natoms;i ++)
      {
        if (!ifs.getline(buffer,BUFF_SIZE))
          return(false);
        tokenize(vs,buffer);
        if (vs.size() < 4)
          return(false);
        if (vs[0].size() > 1)
          vs[0][1] = tolower(vs[0][1]);
        atom = mol.NewAtom();
        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); //set coordinates
        atom->SetAtomicNum(etab.GetAtomicNum(vs[0].c_str()));

        for (j = vs.begin()+4;j != vs.end();j++)
          mol.AddBond(atom->GetIdx(),atoi((char*)j->c_str()),1);
      }
    
    // clean out any remaining blank lines
    while(ifs.peek() != EOF && ifs.good() && 
          (ifs.peek() == '\n' || ifs.peek() == '\r'))
      ifs.getline(buffer,BUFF_SIZE);

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

bool ReadAlchemy(istream &ifs,OBMol &mol, const char *title)
{
  int i;
  int natoms,nbonds;
  char buffer[BUFF_SIZE];

  ifs.getline(buffer,BUFF_SIZE);
  sscanf(buffer,"%d %*s %d", &natoms, &nbonds);
  if (!natoms) return(false);

  mol.ReserveAtoms(natoms);
  ttab.SetFromType("ALC");

  string str;
  double x,y,z;
  OBAtom *atom;
  vector<string> vs;

  for (i = 1; i <= natoms; i ++)
  {
    if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
    tokenize(vs,buffer);
    if (vs.size() != 6) return(false);
    atom = mol.NewAtom();
    x = atof((char*)vs[2].c_str());
    y = atof((char*)vs[3].c_str());
    z = atof((char*)vs[4].c_str());
    atom->SetVector(x,y,z); //set coordinates

    //set atomic number
    ttab.SetToType("ATN"); ttab.Translate(str,vs[1]);
    atom->SetAtomicNum(atoi(str.c_str()));
    //set type
    ttab.SetToType("INT"); ttab.Translate(str,vs[1]); 
    atom->SetType(str);
  }

  char bobuf[100];
  string bostr;
  int bgn,end,order;

  for (i = 0; i < nbonds; i++)
  {
    if (!ifs.getline(buffer,BUFF_SIZE)) return(false);
    sscanf(buffer,"%*d%d%d%s",&bgn,&end,bobuf);
    bostr = bobuf; order = 1;
    if      (bostr == "DOUBLE")   order = 2;
    else if (bostr == "TRIPLE")   order = 3;
    else if (bostr == "AROMATIC") order = 5;
    mol.AddBond(bgn,end,order);
  }

  mol.SetTitle(title);
  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 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);
}

void testIdsAddAtom()
{
  OBMol mol;
  // add 5 atoms
  for (int i = 0; i < 5; ++i)
    mol.NewAtom();

  OBAtom a;
  a.SetAtomicNum(6);
  // add a sixth atom
  mol.AddAtom(a);

  OB_REQUIRE( mol.NumAtoms() == 6 );
  OB_REQUIRE( mol.GetAtomById(5) );
  OB_REQUIRE( mol.GetAtomById(5)->GetId() == 5 );
}

void AliasData::DeleteExpandedAtoms(OBMol& mol)
{
  //The atom that carries the AliasData object remains as an Xx atom with no charge;
  //the others are deleted. All the attached hydrogens are also deleted.
  for(unsigned i=0;i<_expandedatoms.size();++i)
  {
    OBAtom* at = mol.GetAtomById(_expandedatoms[i]);
    if(!at)
      continue;
    mol.DeleteHydrogens(at);
    if(at->HasData(AliasDataType))
    {
      at->SetAtomicNum(0);
      at->SetFormalCharge(0);
      at->SetSpinMultiplicity(0);
    }
    else
      mol.DeleteAtom(at);
  }
  _expandedatoms.clear();
}

  bool MacroModFormat::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();
    OBMol &mol = *pmol;
    const char* defaultTitle = pConv->GetTitle();

    // Get Title
    char buffer[BUFF_SIZE];
    int natoms;
    vector<vector<pair<int,int> > > connections;

    if (ifs.getline(buffer,BUFF_SIZE))
      {
        vector<string> vs;
        tokenize(vs,buffer," \n");

        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++)
//.........这里部分代码省略.........