[Biopython-dev] RFC: RNAStructure package for BioPython

[Kristian Rother]

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 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.

Best Regards,
    Kristian Rother
    www.rubor.de

   Structural Bioinformatics Group
   UAM Poznan