Thanks a lot for your answer, I have been able to solve my problem. I
had not understood previously what OBResidue could do. Concerning
GetAminoAcid and GetTypeFromPDB, my mail was not clear. These
functions don't exist but I was looking for similar functions.
If later people have the same issues as mines in C++, here is what I did:
// First, load protein.pdb in obMol.
unsigned int counterAtom=0;
for (unsigned int i=0 ; i < obMol.NumResidues() ; i++) {
OpenBabel::OBResidue *obResidue;
obResidue = obMol.GetResidue(i);
for (unsigned int j=1 ; j <= obResidue->GetNumAtoms() ; j++) {
OpenBabel::OBAtom *atom;
atom = obMol.GetAtom(counterAtom+j);
cout << obResidue->GetName() << " " <<
obResidue->GetAtomID(atom) << "\t" << obResidue->GetSerialNum(atom) <<
"\t" << atom->GetX() << " " << atom->GetY() << " " << atom->GetZ() <<
endl;
}
counterAtom += obResidue->GetNumAtoms() ;
}
Nicolas
2014-06-06 4:28 GMT-04:00 Pascal Muller <pascal.jm.mul...@gmail.com>:
> 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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