Re: Deprecating Bio.PDB.PSEA
Peter Cock <[email protected]> Thu, 27 Jul 2017 15:58:53 +0100
| Newsgroups | gmane.comp.python.bio.devel |
|---|---|
| Message-ID | <CAKVJ-_5G2V_LJekOnvvc6U04P6FmATgbcvD_S-GQ4LhuX4EEjw@mail.gmail.com> |
Thanks Patrick, Sourav - If there are no objections, then next week I suggest you make a pull request to do the deprecation. Regards, Peter On Thu, Jul 27, 2017 at 3:30 PM, Patrick Kunzmann <[email protected]> wrote: > 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 <[email protected]> >> 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. >>> >>> _______________________________________________ >>> Biopython-dev mailing list >>> [email protected] >>> http://mailman.open-bio.org/mailman/listinfo/biopython-dev >> >> _______________________________________________ >> Biopython-dev mailing list >> [email protected] >> http://mailman.open-bio.org/mailman/listinfo/biopython-dev > > > _______________________________________________ > Biopython-dev mailing list > [email protected] > http://mailman.open-bio.org/mailman/listinfo/biopython-dev