[Biopython-dev] Deprecating Bio.PDB.PSEA

Peter Cock p.j.a.cock at googlemail.com
Thu Jul 27 08:50:15 UTC 2017

This came up in discussion on this pull request:


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


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
> 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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> Biopython-dev at mailman.open-bio.org
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