[Biopython-dev] RFC: RNAStructure package for BioPython

[Peter]

On Mon, Aug 3, 2009 at 4:11 PM, Kristian Rother<krother at rubor.de> wrote:
> Hi,
>
> We have created a lot of code that works on RNA structures in Poznan,
> Poland. There are some jewels that I consider useful and mature enough to
> meet a wider audience. I'd be interested in refactorizing and packaging them
> as a RNAStructure package and contribute it to BioPython.

I remember we talked about this briefly at BOSC/ISMB - it sounds good.
Did you get a chance to talk to Thomas Hamelryck about this?

> I just discussed the possibilities with Magdalena Musielak & Tomasz Puton
> who wrote & tested significant portions of the code. They came up with a
> list of 'most wanted' Use Cases:
>
> - Calculate RNA base pairs
> - Generate RNA secondary structures from 3D structures
> - Recognize pseudoknots
> - Recognize modified nucleotides in RNA 3D structures.
> - Superimpose two RNA molecules.
>
> The existing code massively uses Bio.PDB already, and has little
> dependancies apart from that.
>
> Any comments how this kind of functionality would fit into BioPython are
> welcome.

I see you have already started a github branch, which is great:
http://github.com/krother/biopython/tree/rol

Am I right in thinking all of this code is for 3D RNA work? Maybe that
might give a good module name... Bio.RNA3D? Or Bio.PDB.RNA?
Did you  have something in mind?

Peter

P.S. Who won the ISMB Art and Science Exhibition  prize?
http://www.iscb.org/ismbeccb2009/artscience.php