[Biopython] Structure Module

[Peter Cock]

Hi Patrick,

I see you saw my comment on GitHub about trying to use PEP8
lower case modules for new areas of Biopython, thus here
Bio.structure - thank you.

Did you see any of the past mailing list discussions about how
a Bio.structure might look - taking into account the range of file
formats (especially now that the text based PDB format is itself
deprecated), perhaps following the high-level file format neutral
parser API style used in SeqIO, AlignIO, SearchIO, Phylo, etc?

Or is your work here more focused on the alternative data model
(replacing the Bio.PDB object hierarchy)?

Kind regards,

Peter


On Sat, May 27, 2017 at 9:50 AM, Patrick Kunzmann
<padix.kleber at gmail.com> wrote:
> Hi at all,
>
> I'd like to present you a subpackage, I wrote for Biopython. This
> "structure" package contains functionality for protein structure analysis.
> Now you may ask: "Where is the benefit over the PDB package?".  In the new
> package, a structure is represented by numpy arrays, which enables
> convenient and fast data handling. If you are interested, check out the
> corresponding branch in my Biopython fork.
>
> https://github.com/padix-key/biopython/tree/numpy-structure
>
> or look into the documentation I created using Sphinx
>
> https://github.com/padix-key/biopython/files/1033426/doc.zip
>
> This project is still work in progress and I am open for suggestions,  bug
> reports or contributions.
>
> Best regards,
> Patrick Kunzmann
>
>
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