[Biopython] Structure Module

[Patrick Kunzmann]

Since I joined the mailing lists recently, I have not seen the 
discussion yet. The primary aim of the package is efficient and easy 
structure data analysis. An "structure.io" subpackage is also planned 
for the future, where the structures can be read and written from/to 
different file formats, but this might require some support from the 
Biopython community.

Best regards,

Patrick


Am 29.05.2017 um 12:26 schrieb 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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