Hi,
I’m trying to write a pdb file by using OBMol, OBAtom,... class in c++.
I only have a problem to define the name of the atoms. I need to choice
myself there names.
For this I use SetType of OBAtom :
OBAtom *Atom;
Atom→SetType(NewName[i]); // NewName[i] is a string
The command Atom→GetType() works well and return the good name but nothing
is written in the pdb file at the place of atom name ( column 3 ). Thus I
think that SetType is not the attribute used to put the name of the atom in
the pdb format.
How does work the attribution of the atom name in the pdb format? What
should I do to provide the name of the atom and write well the column 3 of
the pdb file ?
Greetings, Ivan
OBMol mol;
OBFormat *format;
OBConversion conv;
conv.SetOutFormat("pdb");
mol.BeginModify()
for (int i=0;i<ResiduIndex.size();i++)
{
item=i;
if ( std::find(atom.begin(), atom.end(), item) != atom.end() )
{
}
else
{
OBAtom *Atom;
OBResidue *Residu;
Residu=mol.NewResidue();
Atom=mol.NewAtom();
atom.push_back(i);
countAtom++;
countResidu++;
Atom->SetResidue(Residu);
Atom->SetType(NewName[i]);
Residu->SetName(AtomInResidu[i]);
Residu->SetNum(countResidu);
Atom->SetVector(coord[stepInitial][i][0],coord[stepInitial][i][1],coord[stepInitial][i][2]);
cout << Atom->GetIdx() << " " << Atom->GetType() << " " <<
Residu->GetName() << " " << Residu->GetIdx() << " " << Atom->GetVector() <<
endl ;
}
mol.EndModify();
conv.Write(&mol,&monFlux);
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