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

[Peter Cock]

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