[Biopython-dev] RFC: RNAStructure package for BioPython

[Brad Chapman]

Hi Kristian;

> 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.

This sounds great. I don't know enough about the area to comment
directly on your use cases -- my experience is limited to folding
structures with RNAFold and the like -- but it sounds like a solid
feature set.

> 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.

You may also want to have a look at PyCogent, which has wrappers and
parsers for several command line programs involved with RNA structure, 
along with a representation of RNA secondary structure:

http://pycogent.svn.sourceforge.net/viewvc/pycogent/trunk/cogent/struct/rna2d.py?view=markup

It would be great to complement this functionality, and interact
with PyCogent where feasible.

We could offer more specific suggestions as you get rolling with this
and there is code to review. Glad to have you interested,
Brad