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())];
}
}
/*
// 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")
{
buf = _pxmlConv->GetAttribute("ID");
if (buf.length())
{
}
}
else if(name=="tableCell")
{
buf = _pxmlConv->GetAttribute("value");
if (buf.length())
{
}
}
*/
return true;
}
