atom.GetResidue() has the PDB information.
for atom in ob.OBMolAtomIter(mol.OBMol):
residue = atom.GetResidue()
print("%d %s %s" % (residue.GetIdx(), residue.GetName(),
residue.GetAtomID(atom)))
Regarding addh(), I'm not sure what DSSP is.
On Sun, 16 Feb 2020 at 15:40, Athanasios Anastasiou <athanastas...@gmail.com>
wrote:
> Hello
>
> I am trying to obtain some information from a PDB file, using openbabel,
> but I find myself going in a roundabout way getting it....and this is not a
> good sign, so I was wondering if I could get some help around the following
> (?):
>
> 1. Having read a PDB and obtained a reference to a pybel.Atom / OBAtom,
> which attribute corresponds to the "Element Symbol" of the ATOM record?
> Alternatively, what would be a generic way of inferring it from the "type"?
> Is it always "[A-Z][a-z]*[0-9]+"?
>
> 2. Alternatively to 1, how can I select all atoms that belong to a main
> chain of a molecule?
>
> 3. How close is the "addh()" function to the way the DSSP works? Once
> "addh()" is called, hydrogens are added and their bond lengths are worked
> out. Each "H" is marked as a "donor_h" and adjacent atoms are marked with
> donor / acceptor attributes. However, that "H" appears to be attached only
> on one side (to its donor) and the acceptor is flagged but not "attached".
> Would I be too wrong if I run a "nearest neighbour that is also acceptor"
> query and "attach" it myself? And if I was to do this wouldn't I now know
> where the hydrogen bonds are and from the respective distances to all known
> atoms, be able to work out its energy (?). (Just as DSSP does).
>
> 4. There are H Bonds that are also flagged away from (what I think is) the
> main chain of a molecule. In one example, there are two H that are flagged
> as the hbond_donor_h's which are attached to a "Nam" (?) that is marked as
> "donor". This in turn is attached to a C and that C is also attached to an
> O. That O is marked as an "acceptor". What happens in that case? Would I
> simply ignore that or attempt to still go ahead and infer a bond?
>
> All the best
> thanOS
>
>
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