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

[Kristian Rother]

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


>> Hi Peter,
>>
>> just digesting BioPy mails from last week.
>>
>>>> Where should the str subclass for secondary structures that the
>>>> parsers
>>>> create go? Could it be Bio.Struct.RNA?
>>>
>>> You don't think plain strings in the SeqRecord's letter_annotation
>>> dict would be enough?
>>
>> Not really - base pairing makes most normal string functions useless.
>>
>>
>>> Assuming you do need something then
>>> perhaps under Bio.Seq or Bio.SeqUtils might be worth considering
>>> as alternatives to Bio.Struct.RNA.
>>
>> OK, I'll try that.
>>
>> Thanks,
>>   Kristian
>>
>>
>
> Hi Kristian,
>
> Could you explain at little more about why plain strings wouldn't be
> suitable here. What kind of things do you want to do with them?
>
> Peter
>
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