[Biopython-dev] [biopython] Fix flex library dependency of MMCIFlex; closes 2619 (#31)

[João Rodrigues]

Great work Lenna, thanks for taking care of this!

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



No dia 29 de Março de 2012 16:04, Lenna Peterson <arklenna at gmail.com>escreveu:

> Hi Peter,
>
> Sounds great. Thanks for the update.
>
> As far as I can tell, the only thing string.letters is used for is the
> PDB iCode. I'm fairly certain the iCode allows only ASCII letters, so
> string.ascii_letters should be fine.
>
> Lenna
>
> On Thu, Mar 29, 2012 at 9:17 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> > On Fri, Mar 23, 2012 at 11:52 PM, Lenna Peterson <arklenna at gmail.com>
> wrote:
> >> Hi Peter,
> >>
> >> I've added a unit test (Tests/test_MMCIF.py). It currently tests
> >> whether a polypeptide is extracted properly.
> >
> > Lovely - I've cherry-picked that (two commits) to the master branch,
> > and made sure it is skipped gracefully if the C code is not being
> > compiled (still the default). I'll then have a go on a few different
> > platforms to check everything is working as expected.
> >
> > One thing I did spot breaks under Python 3 is this line in
> > Bio/PDB/MMCIFParser.py,
> >
> > from string import letters
> >
> > Quoting: http://docs.python.org/release/3.1.3/whatsnew/3.0.html
> >>> string.letters and its friends (string.lowercase and string.uppercase)
> >>> are gone. Use string.ascii_letters etc. instead. (The reason for the
> >>> removal is that string.letters and friends had locale-specific
> behavior,
> >>> which is a bad idea for such attractively-named global “constants”.)
> >
> > Do you see any risk with switching this to string.ascii_letters instead?
> >
> > Peter
>
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