[Biopython-dev] RNA module contributions

[Kristian Rother]

Hi,

to start work on RNA modules, I'd like to contribute some of our tested 
modules to BioPython. Before I place them into my GIT branch, it would 
be great to get some comments:

Bio.RNA.SecStruc
    - represents a RNA secondary structures,
    - recognizing of SSEs (helix, loop, bulge, junction)
    - recognizing pseudoknots

Bio.RNA.ViennaParser      
    - parses RNA secondary structures in the Vienna format into SecStruc 
objects.

Bio.RNA.BpseqParser       
    - parses RNA secondary structures in the Bpseq format into SecStruc 
objects.

Connected to RNA, but with a wider focus:

Bio.???.ChemicalGroupFinder
    - identifies chemical groups (ribose, carboxyl, etc) in a molecule 
graph (place to be defined yet)

There is a contribution from Bjoern Gruening as well:

Bio.PDB.PDBMLParser
    - creates PDB.Structure objects from PDB-XML files.


Comments and suggestions welcome!

Best Regards,
    Kristian Rother