[Biopython-dev] Features of the GSOC branch ready to be merged

[Eric Talevich]

On Tue, Nov 30, 2010 at 10:45 AM, João Rodrigues <anaryin at gmail.com> wrote:

> Hello all,
>
> I've been looking at the code I wrote for the GSOC to see what is ready to
> be merged in the main branch. I have to thank Kristian and whoever
> participated in the Python & Friends for the input.
>
>
Hi João,

It sounds like everyone is happy with this branch:
https://github.com/JoaoRodrigues/biopython/tree/atom-element

So I will try to fetch your branch, correct the spelling of the
IUPACData.atom_weights references (unless you beat me to it), test, rebase
onto biopython/biopython/master, and merge it this weekend.

Regarding the other two stable features:

- renumber_residues looks simple and useful; I'm looking forward to having
that feature on the biopython trunk. A labmate of mine recently had a
problem where he wanted to renumber just a portion of the residues in a
structure -- I don't think we need to extend the function to that use case,
though.

- biological_unit: I still haven't tried this one myself. Does it work well
enough for your needs? Using models to represent each unit of the assembly
is the concept I want to be sure about -- e.g. will we be able to detect
hydrogen bonds between units, or at least calculate distances between atoms
in different units? We talked about creating new chain IDs as an alternative
at one point, and iirc the issue was that the original structure might have
multiple chains, and the names could collide. Are chain names restricted to
single alphabetical characters, and if not, could you get the same effect
with appending numbers to the original chain ID, e.g. A -> A0, A1, A2, ... ?
(Sorry to rehash this.)

Thanks for all your work on this project.

-Eric