C++ OBAtom::GetPartialCharge方法代码示例

 void OBChargeModel::FillChargeVectors(OBMol &mol)
 {
   OBAtom *atom;
   vector<OBAtom*>::iterator itr;
   m_partialCharges.clear();
   m_partialCharges.reserve(mol.NumAtoms());
   m_formalCharges.clear();
   m_formalCharges.reserve(mol.NumAtoms());
   
   for (atom = mol.BeginAtom(itr);atom;atom = mol.NextAtom(itr))
     {
       m_partialCharges.push_back(atom->GetPartialCharge());
       m_formalCharges.push_back((double)(atom->GetFormalCharge()));
     }
 }

  void ReportFormat::WriteCharges(ostream &ofs,OBMol &mol)
  {
    unsigned int i;
    OBAtom *atom;
    char buffer[BUFF_SIZE];

    for(i = 1;i <= mol.NumAtoms(); i++)
      {
        atom = mol.GetAtom(i);
        snprintf(buffer, BUFF_SIZE, "%4s%4d   % 2.10f",
                OBElements::GetSymbol(atom->GetAtomicNum()),
                i,
                atom->GetPartialCharge());

        ofs << buffer << "\n";
      }
  }

  void WriteCharges(ostream &ofs,OBMol &mol)
  {
    unsigned int i;
    OBAtom *atom;
    char buffer[BUFF_SIZE];
    
    for(i = 1;i <= mol.NumAtoms(); i++)
      {
	atom = mol.GetAtom(i);
	sprintf(buffer,"%4s%4d   % 2.10f",
		etab.GetSymbol(atom->GetAtomicNum()),
		i,
		atom->GetPartialCharge());
	
	ofs << buffer << endl;
      }
  }

bool WriteHIN(ostream &ofs,OBMol &mol)
{
  unsigned int i, file_num = 1;
  string str,str1;
  char buffer[BUFF_SIZE];
  OBAtom *atom;
  OBBond *bond;
  vector<OBEdgeBase*>::iterator j;
  char bond_char;

  ofs << "mol " << file_num << " " << mol.GetTitle() << endl;;
  for(i = 1;i <= mol.NumAtoms(); i++)
  {
    atom = mol.GetAtom(i);
    sprintf(buffer,"atom %d - %-3s **  - %8.5f %8.5f  %8.5f  %8.5f %d ",
	    i,
	    etab.GetSymbol(atom->GetAtomicNum()),
	    atom->GetPartialCharge(),
	    atom->GetX(),
	    atom->GetY(),
	    atom->GetZ(),
	    atom->GetValence());
    ofs << buffer;
    for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
    {
      switch(bond->GetBO())
      {
      case 1 : bond_char = 's'; break;
      case 2 : bond_char = 'd'; break;
      case 3 : bond_char = 't'; break;
      case 5 : bond_char = 'a'; break;
      default: bond_char = 's'; break;
      }
      sprintf(buffer,"%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);
      ofs << buffer;
    }
    ofs << endl;
  }
  ofs << "endmol " << file_num << endl;
  return(true);
}

  bool MOL2Format::WriteMolecule(OBBase* pOb, OBConversion* pConv)
  {
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
      return false;

    //Define some references so we can use the old parameter names
    ostream &ofs = *pConv->GetOutStream();
    OBMol &mol = *pmol;
    bool ligandsOnly = pConv->IsOption("l", OBConversion::OUTOPTIONS)!=NULL;
 
    //The old code follows....
    string str,str1;
    char buffer[BUFF_SIZE],label[BUFF_SIZE];
    char rnum[BUFF_SIZE],rlabel[BUFF_SIZE];

    ofs << "@<TRIPOS>MOLECULE" << endl;
    str = mol.GetTitle();
    if (str.empty())
      ofs << "*****" << endl;
    else
      ofs << str << endl;

    snprintf(buffer, BUFF_SIZE," %d %d 0 0 0", mol.NumAtoms(),mol.NumBonds());
    ofs << buffer << endl;
    ofs << "SMALL" << endl;

    OBPairData *dp = (OBPairData*)mol.GetData("PartialCharges");
    if (dp != NULL) {
        // Tripos spec says:
        // NO_CHARGES, DEL_RE, GASTEIGER, GAST_HUCK, HUCKEL, PULLMAN, 
        // GAUSS80_CHARGES, AMPAC_CHARGES, MULLIKEN_CHARGES, DICT_ CHARGES,
        // MMFF94_CHARGES, USER_CHARGES
      if (dp->GetValue() == "Mulliken")
        ofs << "MULLIKEN_CHARGES" << endl;
      else // should pick from the Tripos types
        ofs << "GASTEIGER" << endl;
    }
    else { // No idea what these charges are... all our code sets "PartialCharges"
        ofs << "GASTEIGER" << endl;
    }

    ofs << "Energy = " << mol.GetEnergy() << endl;

    if (mol.HasData(OBGenericDataType::CommentData))
      {
        OBCommentData *cd = (OBCommentData*)mol.GetData(OBGenericDataType::CommentData);
        ofs << cd->GetData();
      }

    ofs << endl;
    ofs << "@<TRIPOS>ATOM" << endl;

    OBAtom *atom;
    OBResidue *res;

    vector<OBAtom*>::iterator i;
    vector<int> labelcount;
    labelcount.resize( etab.GetNumberOfElements() );

    ttab.SetFromType("INT");
    ttab.SetToType("SYB");

    for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
      {

        //
        //  Use sequentially numbered atom names if no residues
        //

        snprintf(label,BUFF_SIZE, "%s%d",
                 etab.GetSymbol(atom->GetAtomicNum()),
                 ++labelcount[atom->GetAtomicNum()]);
        strcpy(rlabel,"<1>");
        strcpy(rnum,"1");

        str = atom->GetType();
        ttab.Translate(str1,str);

        //
        //  Use original atom names if there are residues
        //

        if (!ligandsOnly && (res = atom->GetResidue()) )
          {
            // use original atom names defined by residue
            snprintf(label,BUFF_SIZE,"%s",(char*)res->GetAtomID(atom).c_str());
            // make sure that residue name includes its number
            snprintf(rlabel,BUFF_SIZE,"%s%d",res->GetName().c_str(), res->GetNum());
            snprintf(rnum,BUFF_SIZE,"%d",res->GetNum());
          }

        snprintf(buffer,BUFF_SIZE,"%7d%1s%-6s%12.4f%10.4f%10.4f%1s%-5s%4s%1s %-8s%10.4f",
                 atom->GetIdx(),"",label,
                 atom->GetX(),atom->GetY(),atom->GetZ(),
                 "",str1.c_str(),
                 rnum,"",rlabel,
                 atom->GetPartialCharge());
        ofs << buffer << endl;
      }
//.........这里部分代码省略.........

  bool BGFFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
  {
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
      return false;

    //Define some references so we can use the old parameter names
    ostream &ofs = *pConv->GetOutStream();
    OBMol &mol = *pmol;

    vector<OBAtom*>::iterator i;
    int max_val;
    OBAtom *atom;
    char buffer[BUFF_SIZE];
    char elmnt_typ[8], dreid_typ[8], atm_sym[16], max_val_str[8];

    mol.Kekulize();

    ofs << "BIOGRF 200\n";
    snprintf(buffer, BUFF_SIZE, "DESCRP %s\n",mol.GetTitle());
    ofs << buffer;
    snprintf(buffer, BUFF_SIZE, "REMARK BGF file created by Open Babel %s\n",BABEL_VERSION);
    ofs << "FORCEFIELD DREIDING  \n";

    // write unit cell if available
    if (mol.HasData(OBGenericDataType::UnitCell))
      {
        OBUnitCell *uc = (OBUnitCell*)mol.GetData(OBGenericDataType::UnitCell);
        // e.g. CRYSTX    49.30287   49.23010   25.45631   90.00008   89.99995   57.10041
        snprintf(buffer, BUFF_SIZE,
                 "CRYSTX%12.5f%12.5f%12.5f%12.5f%12.5f%12.5f",
                 uc->GetA(), uc->GetB(), uc->GetC(),
                 uc->GetAlpha() , uc->GetBeta(), uc->GetGamma());
        ofs << buffer << "\n";
      }

    ofs << "FORMAT ATOM   (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)\n";

    ttab.SetFromType("INT");

    for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
      {
        strncpy(elmnt_typ,etab.GetSymbol(atom->GetAtomicNum()), 7); // make sure to null-terminate
        elmnt_typ[sizeof(elmnt_typ) - 1] = '0';
        ToUpper(elmnt_typ);

        ttab.SetToType("DRE");
        ttab.Translate(dreid_typ,atom->GetType());
        ttab.SetToType("HAD");
        ttab.Translate(max_val_str,atom->GetType());
        max_val = atoi(max_val_str);
        if (max_val == 0)
          max_val = 1;
        snprintf(atm_sym,16,"%s%d",elmnt_typ,atom->GetIdx());
        snprintf(buffer,BUFF_SIZE,"%6s %5d %-5s %3s %1s %5s%10.5f%10.5f%10.5f %-5s%3d%2d %8.5f\n",
                "HETATM",
                atom->GetIdx(),
                atm_sym,
                "RES",
                "A",
                "444",
                atom->GetX(),
                atom->GetY(),
                atom->GetZ(),
                dreid_typ,
                max_val,
                0,
                atom->GetPartialCharge());
        ofs << buffer;
      }
    ofs<< "FORMAT CONECT (a6,12i6)\n\n";

    OBAtom *nbr;
    vector<OBBond*>::iterator j;
    for (atom = mol.BeginAtom(i);atom;atom = mol.NextAtom(i))
      if (atom->GetValence())
        {
          snprintf(buffer,BUFF_SIZE,"CONECT%6d",atom->GetIdx());
          ofs << buffer;
          for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
            {
              snprintf(buffer,BUFF_SIZE,"%6d",nbr->GetIdx());
              ofs << buffer;
            }
          ofs << endl;

          snprintf(buffer,BUFF_SIZE,"ORDER %6d",atom->GetIdx());
          ofs << buffer;
          for (nbr = atom->BeginNbrAtom(j);nbr;nbr = atom->NextNbrAtom(j))
            {
              snprintf(buffer,BUFF_SIZE,"%6d",(*j)->GetBO());
              ofs << buffer;
            }
          ofs << endl;
        }

    ofs << "END" << endl;
    return(true);
  }

  bool HINFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
  {
    OBMol* pmol = dynamic_cast<OBMol*>(pOb);
    if(pmol==NULL)
      return false;

    //Define some references so we can use the old parameter names
    ostream &ofs = *pConv->GetOutStream();
    OBMol &mol = *pmol;

    unsigned int i, file_num = 1;
    string str,str1;
    char buffer[BUFF_SIZE];
    OBAtom *atom;
    OBBond *bond;
    vector<OBBond*>::iterator j;
    char bond_char;

    // make sure to escape titles in double quotes
    // PR#1501694
    ofs << "mol " << file_num << " \"" << mol.GetTitle() << "\"\n";

    for(i = 1;i <= mol.NumAtoms(); i++)
      {
        atom = mol.GetAtom(i);
        snprintf(buffer, BUFF_SIZE, "atom %d - %-3s **  - %8.5f %8.5f  %8.5f  %8.5f %d ",
                i,
                etab.GetSymbol(atom->GetAtomicNum()),
                atom->GetPartialCharge(),
                atom->GetX(),
                atom->GetY(),
                atom->GetZ(),
                atom->GetValence());
        ofs << buffer;
        for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j))
          {
            switch(bond->GetBO())
              {
              case 1 :
                bond_char = 's';
                break;
              case 2 :
                bond_char = 'd';
                break;
              case 3 :
                bond_char = 't';
                break;
              case 5 :
                bond_char = 'a';
                break;
              default:
                bond_char = 's';
                break;
              }
            if (bond->IsAromatic())
              bond_char = 'a';

            snprintf(buffer,BUFF_SIZE, "%d %c ", (bond->GetNbrAtom(atom))->GetIdx(), bond_char);
            ofs << buffer;
          }
        ofs << endl;
      }
    ofs << "endmol " << file_num << endl;
    return(true);
  }