C++ OBAtom::Clear方法代码示例

bool ChemDrawXMLFormat::EndElement(const string& name)
{
    //unsigned int i;
    if(name=="n")
    {
        _pmol->AddAtom(_tempAtom);
        atoms[_tempAtom.GetIdx()] = _pmol->NumAtoms();
        _tempAtom.Clear();
    }
    else if(name=="b")
    {
        _pmol->AddBond(Begin, End, Order, Flag);
        Order = -1;
    }
    else if(name=="fragment") //this is the end of the molecule we are extracting
    {
        EnsureEndElement();
        _pmol->EndModify();

        // This alone will already store the "Formula" property in the molecule property block
        // The "Formula" is required for older ChemDraw generations allowing to match molecules to reaction properties
        string MolFormula=_pmol->GetFormula();

        // additional adding of "Formula" property is not required, as described above
        //OBPairData *dp = new OBPairData;
        //dp->SetAttribute("MolecularFormula");
        //dp->SetValue(MolFormula);
        //dp->SetOrigin(fileformatInput);
        //_pmol->SetData(dp);

        // alternative is using the molecular title, but a test is needed for preventing overwriting given titles, aka molecule ID
        //_pmol->SetTitle(MolFormula);

        atoms.clear();
        return false;//means stop parsing
    }
    /*
    // Forget that, the fragment, aka molecule, is in another XML hierachy tree than the data.
    // Parsing has already stopped before ever getting to this point
    else if(name=="tags")
    {
    }
    else if(name=="tableCell")
    {
      //OBPairData *dp = new OBPairData;
      //dp->SetAttribute(attr);
      //dp->SetValue(buff);
      //dp->SetOrigin(fileformatInput);
      //mol.SetData(dp);
    }*/

    return true;
}

void ChemDrawXMLFormat::EnsureEndElement(void)
{
    if (_tempAtom.GetAtomicNum() != 0)
    {
        _pmol->AddAtom(_tempAtom);
        atoms[_tempAtom.GetIdx()] = _pmol->NumAtoms();
        _tempAtom.Clear();
    }
    else if (Order >= 0)
    {
        _pmol->AddBond(Begin, End, Order, Flag);
        Order = -1;
    }
}

bool ChemDrawXMLFormat::DoElement(const string& name)
{
    string buf;
    if(name=="fragment")
    {
        //This is the start of the molecule we are extracting and it will
        //be put into the OBMol* _pmol declared in the parent class.
        //initialise everything
        _tempAtom.Clear();
        atoms.clear();

        _pmol->SetDimension(2);
        _pmol->BeginModify();

        buf = _pxmlConv->GetAttribute("id");
        if (buf.length())
        {
            _pmol->SetTitle(buf);
        }
    }
    else if(name=="n")
    {
        EnsureEndElement();
        buf = _pxmlConv->GetAttribute("Type");
        if (buf.length())
        {
            if (buf != "Unspecified" && buf != "Element")
            {
                cerr << "CDXML Format: Node type \"" << buf <<
                     "\" is not currently supported." << endl;
                return false; // FIXME: use as many types as possible
            }
        }
        _tempAtom.SetAtomicNum(6); // default is carbon
        buf = _pxmlConv->GetAttribute("id");
        if (buf.length())
            _tempAtom.SetIdx(atoi(buf.c_str()));
        buf = _pxmlConv->GetAttribute("Element");
        if (buf.length())
            _tempAtom.SetAtomicNum(atoi(buf.c_str()));

        buf = _pxmlConv->GetAttribute("p"); // coords
        if (buf.length())
        {
            double x = 0., y = 0.;
            sscanf(buf.c_str(), "%lf %lf", &x, &y);
            _tempAtom.SetVector(x, y, 0.);
        }
        buf = _pxmlConv->GetAttribute("Charge");
        if (buf.length())
            _tempAtom.SetFormalCharge(atoi(buf.c_str()));
    }
    else if(name=="b")
    {
        EnsureEndElement();
        bool invert_ends = false;
        Begin = End = Flag = 0;
        buf = _pxmlConv->GetAttribute("Order");
        if (buf.length())
            Order = atoi(buf.c_str());
        else
            Order = 1; //default value
        buf = _pxmlConv->GetAttribute("Display");
        if (buf.length())
        {
            if (buf == "WedgeEnd")
            {
                invert_ends = true;
                Flag = OB_HASH_BOND;
            }
            else if (buf == "WedgeBegin")
            {
                Flag = OB_HASH_BOND;
            }
            else if (buf == "Hash" ||buf == "WedgedHashBegin")
            {
                Flag = OB_WEDGE_BOND;
            }
            else if (buf == "WedgedHashEnd")
            {
                invert_ends = true;
                Flag = OB_WEDGE_BOND;
            }
        }
        buf = _pxmlConv->GetAttribute("B");
        if (buf.length())
        {
            if (invert_ends)
                End = atoms[atoi(buf.c_str())];
            else
                Begin = atoms[atoi(buf.c_str())];
        }
        buf = _pxmlConv->GetAttribute("E");
        if (buf.length())
        {
            if (invert_ends)
                Begin = atoms[atoi(buf.c_str())];
            else
                End = atoms[atoi(buf.c_str())];
        }
//.........这里部分代码省略.........

bool CCCFormat::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;
    mol.SetTitle( pConv->GetTitle()); //default title is the filename

    char buffer[BUFF_SIZE];
    ifs.getline(buffer,BUFF_SIZE);

    if (strlen(buffer) > 5)
        mol.SetTitle(&buffer[5]);
    mol.SetEnergy(0.0);

    int natoms;
    ifs.getline(buffer,BUFF_SIZE);
    sscanf(buffer,"%*s%d",&natoms);
    mol.ReserveAtoms(natoms);
    mol.BeginModify();

    int end,order;
    double x,y,z;
    OBAtom atom;
    vector3 v;
    vector<string> vs;
    char element[3];
    element[2] = '\0';

    for (int i = 1;i <= natoms;i++)
    {
        if (!ifs.getline(buffer,BUFF_SIZE))
            return(false);
        atom.Clear();
        element[0] = buffer[0];
        element[1] = (buffer[1] != ' ') ? buffer[1]:'\0';
        atom.SetAtomicNum(etab.GetAtomicNum(element));
        sscanf(&buffer[15],"%lf%lf%lf",&x,&y,&z);
        v.Set(x,y,z);
        atom.SetVector(v);

        if (!mol.AddAtom(atom))
            return(false);
        tokenize(vs,&buffer[60]);
        vector<string>::iterator j;

        for (j = vs.begin();j != vs.end();j++)
            if (!j->empty())
            {
                //get the bond order
                switch((char)(*j)[j->size()-1])
                {
                case 'S':
                    order = 1;
                    break;
                case 'D':
                    order = 2;
                    break;
                case 'T':
                    order = 3;
                    break;
                default:
                    order = 1;
                }
                (*j)[j->size()-1] = ' ';
                end = atoi(j->c_str());
                if (i>end)
                    mol.AddBond(i,end,order);
            }
    }

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

bool TurbomoleFormat::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;
    double UnitConv=AAU;
    if(pConv->IsOption("a", OBConversion::INOPTIONS))
      UnitConv=1;


    char buffer[BUFF_SIZE];
    do
    {
        ifs.getline(buffer,BUFF_SIZE);
	if (ifs.peek() == EOF || !ifs.good())
	  return false;
    }
    while(strncmp(buffer,"$coord",6));

    mol.BeginModify();
    OBAtom atom;
    while(!(!ifs))
    {
        ifs.getline(buffer,BUFF_SIZE);
        if(*buffer=='$')
            break;
        if(*buffer=='#')
            continue;
        float x,y,z;
        char atomtype[8];
        if(sscanf(buffer,"%f %f %f %7s",&x,&y,&z,atomtype)!=4)
            return false;

        atom.SetVector(x*UnitConv, y*UnitConv, z*UnitConv);
        atom.SetAtomicNum(OBElements::GetAtomicNum(atomtype));
        atom.SetType(atomtype);

        if(!mol.AddAtom(atom))
            return false;
        atom.Clear();
    }
    while(!(!ifs) && strncmp(buffer,"$end",4))
        ifs.getline(buffer,BUFF_SIZE);

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

    // clean out remaining blank lines
    std::streampos ipos;
    do
    {
      ipos = ifs.tellg();
      ifs.getline(buffer,BUFF_SIZE);
    }
    while(strlen(buffer) == 0 && !ifs.eof() );
    ifs.seekg(ipos);

    mol.EndModify();
    return true;
}