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

Lenna Peterson arklenna at gmail.com
Thu Mar 22 23:15:44 UTC 2012

Hi Peter,

As far as I can tell, there isn't an MMCIF unit test. I'll work on a
minimal data file for testing MMCIFParser and MMCIF2Dict - may take me
a day or so as I'm not yet familiar with the unittest class.

Your error indicates that the C module isn't installed (the biopython
site package should contain Bio/PDB/mmCIF/MMCIFlex.so).

Re: Python 3, are you referring to the changes to import?


On Thu, Mar 22, 2012 at 7:18 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi Lenna,
> Sorry for the delay, I thought I wrote this on the github pull request.
> This may be a silly question, but do we have any unit tests for MMCIF?
> I had a quick look yesterday and couldn't see any. I would be much
> happier with a basic unit test so I can check the functionality before
> and after your fix. Hopefully you can come up with a small data file
> and a minimal bit of code to check the parser, which we can turn
> into a new unit test, say test_MMCIF.py
> Also should this work?
>>>> from Bio.PDB import MMCIF2Dict
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "Bio/PDB/MMCIF2Dict.py", line 10, in <module>
>    import Bio.PDB.mmCIF.MMCIFlex as MMCIFlex
> ImportError: No module named MMCIFlex
> [We can post-pone Python 3 support to a new issue]
> Peter

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