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

Peter biopython at maubp.freeserve.co.uk
Tue Jun 1 11:42:53 UTC 2010

2010/6/1 Kristian Rother <krother at rubor.de>:
>> 3. Kristian asked on this list awhile ago about the proper location for
>> his new code that works with RNA structures. While RCSB's PDB
>> contains some RNA structures, the RNA world doesn't revolve around
>> it. Similarly, João needs a place to put code for structure prediction/
>> validation servers, command-line wrappers, secondary structures, etc.
>> I propose a new sub-package called Bio.Struct for these enhancements:
>> from Bio.Struct import RNA
>> # Would this work for you, Kristian?
> Yes, it would be more descriptive than the originally proposed Bio.RNA . I
> am just concerned whether I could keep the 2D structure-related modules
> in the same package.

I don't necessarily see a problem with Bio.Struct or Bio.Structure covering
both 2D and 3D structures. Does this 2D stuff include file parsers? That
would complicate plans for Bio.Struct.read() etc. Maybe Bio.RNA is better.


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