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

[Peter]

On Mon, Jun 14, 2010 at 3:43 PM, Kristian Rother <krother at genesilico.pl> wrote:
>
>
> 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