[Biopython-dev] Deprecating Bio.PDB.PSEA

[Patrick Kunzmann]

There are also no objections from my side. If the algorithm is well 
documented and implementation using numpy arrays is feasible, I might 
integrate it in my onging develoment of a new structure subpackage.

Best regards,

Patrick


On 27.07.2017 10:50, Peter Cock wrote:
> This came up in discussion on this pull request:
>
> https://github.com/biopython/biopython/pull/1336
>
> Quoting the tool's README file,
>
> "P-SEA is small tool for secondary structure assignment
> from Ca cartesian coordinates of proteins. It reads
> PDB-formatted file and return a file containing : the
> sequence read in one-letter code and the secondary
> structure assigned (a=helix, b=strand, c=coil)."
>
> It does compile fine on macOS Sierra, and the readme
> talks about other Unix platforms (HP-UX and IRIX),
> but it does not compile as is on Linux.
>
> In either case you get warnings about using the "gets"
> function which is not secure.
>
> I favour deprecating Bio.PDB.PSEA
>
> Peter
>
>
> On Wed, Jul 26, 2017 at 7:13 PM, Sourav Singh <ssouravsingh12 at gmail.com> wrote:
>> Hello,
>>
>> As referenced in the subject, I would like to discuss about deprecating
>> Bio.PDB.PSEA
>>
>> As referenced in the link here-
>> ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/P-SEA.tar.gz
>>
>> The last update to the P-SEA package was done in September 1996, which makes
>> it really old. I would like to know if the dev community is fine with
>> deprecating the module for future releases of Biopython.
>>
>> Regards,
>>
>> Sourav
>>
>> Sent from my Phone.Excuse any mistakes and brevity.
>>
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