[Biopython-dev] upcoming Bio.PDB enhancements - RNA

[Peter]

On Mon, Jun 14, 2010 at 4:01 PM, Kristian Rother <krother at rubor.de> wrote:
>
> Hi,
>
> much of what I do with RNA secondary structures strongly depends on
> iterating base pairs, e.g..
>
>>>> sec = Secstruc("(((...)).)")
>>>> for bp in sec.basepairs():
>>>>    print bp
> (0, 9)
> (1, 7)
> (2, 6)
>
> also:
>>>> sec.get_helices()
>>>> sec.get_bulges()
>>>> sec.get_hairpins()
>>>> sec.contains_pseudoknot()
> .. and a couple of similar ones.
>
> The reason why I'd prefer to have something more than a string as a sec
> feature is that I wouldn't want to do all the time:
>
> sec = Secstruc(my_seq['secondary_structure'])
> sec.get_helices()
>
> but
>
> my_seq['secondary_structure'].get_helices()
>
> instead.
>
> Best Regards,
>   Kristian

That helped - thanks. Does your Secstruc object behave like a Python
sequence (string/list/tuple) in that it has a length and can be sliced (as
if acting on the string representation)? If so then it should be fine to
store in the SeqRecord's letter_annotation dictionary.

Peter