[BioPython] Bio.PDB: possible to obtain chain identifier for atoms?
Christian Meesters
meesters at uni-mainz.de
Fri Aug 17 07:15:39 UTC 2007
Hoi Katie,
apparently, yes. Life can be so easy ...
Thanks,
Christian
On Thu, 2007-08-16 at 15:17 -0400, Katie Edmonds wrote:
> Hi Christian,
>
> are you looking for:
> chain1 = a.get_parent().get_parent()
> ?
>
> Katie
>
> On 8/16/07, Christian Meesters <meesters at uni-mainz.de> wrote:
> Hi All,
>
> I'm trying to build a somewhat bigger app which needs to
> calculate the
> distance distribution function of a protein several times. For
> this
> purpose I re-discovered BioPython today.
> Speed is an issue, but since the protein in question isn't too
> big the
> overhead of Python and BioPython might be tolerable.
>
> Still, in order to speed up my code I would need to access the
> chain
> identifier of atoms within a loop. To illustrate my question
> some
> pseudo-code:
>
> atoms = Selection.unfold_entities(structure, 'A')
> for i, a in enumerate(atoms):
> for b in atoms[i+1:]:
> # do some calculations here ...
>
> Now, I cannot avoid the double loop, but if I could check
> somehow
> whether atoms a and b belong to the same chain (and which) I
> would have
> to do this awkward looping only once this way.
>
> Does anybody know an approach? As far as I understand the code
> of the
> Atom class, there is no direct way, right?
>
> TIA
> Christian
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