Molecule* createLocalMolecule(OpenBabel::OBMol* mol, MoleculeT mType,
const std::string& name, std::string& suffix)
{
//
// Add the suffix as comment data to the actual OBMol object.
//
OpenBabel::OBCommentData* cData = new OpenBabel::OBCommentData();
cData->SetAttribute("Comment");
cData->SetData(suffix);
mol->SetData(cData);
//
// Create this particular molecule type based on the name of the file.
//
if (mType == LINKER)
{
return new Linker(mol, name);
}
else if (mType == RIGID)
{
return new Rigid(mol, name);
}
return 0;
}
Linker::Linker(OpenBabel::OBMol* obmol, const std::string& name) : uniqueFragmentID(-1),
Molecule(obmol, name, LINKER)
{
//
// Acquire the comment data, make a copy, parse that comment.
//
OpenBabel::OBCommentData* comment = static_cast<OpenBabel::OBCommentData*>(obmol->GetData("Comment"));
std::string commentStr = comment->GetData();
parseAppendix(commentStr);
}
Rigid::Rigid(OpenBabel::OBMol* obmol, const std::string& name) : Molecule(obmol, name, RIGID)
{
//
// Acquire the comment data, make a copy, parse that comment.
//
OpenBabel::OBCommentData* comment = static_cast<OpenBabel::OBCommentData*>(obmol->GetData("Comment"));
std::string commentStr = comment->GetData();
parseAppendix(commentStr);
this->rigids.push_back(this);
}
Linker::Linker(OpenBabel::OBMol* obmol, const std::string& name) : Molecule(obmol, name)
{
//
// Acquire the comment data, make a copy, parse that comment.
//
OpenBabel::OBCommentData* comment = static_cast<OpenBabel::OBCommentData*>(obmol->GetData("Comment"));
std::string commentStr = comment->GetData();
parseAppendix(commentStr, obmol->NumAtoms());
// if (Options::OPENBABEL) OBWriter::ScrubAndConvertToSMIInternal(obmol, this->smi);
}