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

[Lenna Peterson]

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