Hi,
I have a protein structure in a .pdb file. In my program (using the
> C++ API), I load it (with obConversion.ReadFile) in a OBMol. What I am
> trying to do next, is to get data from the residues and the atom types
> of the pdb file. For example, let's say I have this line in my file:
>
> ATOM 4 CD PRO A 1 20.835 45.525 -5.625 1.00 0.00
> C
>
> I am looking for a function which will tell me that atom 4 is a CD
> atom from a proline. Perhaps something like:
>
> for (unsigned int j=1; j<=obMol.NumAtoms() ; j++ ) {
> OpenBabel::OBAtom *atom;
> atom = obMol.GetAtom(j);
> atom->GetAminoAcid();
> atom->GetTypeFromPDB();
> ...
> }
>
>
Sorry, I don't know about doing it in C++ (furthermore,I didn't find
"GetTypeFromPDB" in the API, if you can give me the link? thanks !), but
with pybel, you can try:
for mol in pybel.readfile("pdb", filename):
for res in openbabel.OBResidueIter(mol.OBMol):
for atom in openbabel.OBResidueAtomIter(res):
print res.GetName(), res.GetAtomID(atom), res.GetSerialNum(atom)
Output e.g.
PRO CD 806
I guess it could easily be translated in C++.
Best,
Pascal
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