[BioPython] bio.pdb.mmcif does not exist

[Alex Lancaster]

>>>>> "P" == Peter   writes:
>> I have installed Biopython without any problems but when I try tu
>> use the mmcif parser or the mmcif2dict, I have a error saying the
>> mmcif package does not exist.
>> 
>> How can I install this package ?

P> Hi Jean,

P> Are you using Windows, Linux, MacOS, other?  How did you install
P> Biopython? (and out of interest, which version?)

P> As you can read on the download page, you will need flex (The Fast
P> Lexical Analyzer) to compile the Bio.PDB.mmCIF.MMCIFlex module. On
P> Linux (and other Unix like systems) this is actually very straight
P> forward.  This may be the same issue here...

On this issue, it appears that in biopython 1.43 compilation of the
mmCIF module is actually commented-out in the setup.py (which would
account for the lack of the Bio.PDB.mmCIF module noted by Jean, even
if flex was installed).  It was removed in this commit:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/setup.py.diff?r1=1.108&r2=1.109&cvsroot=biopython

with the somewhat confusing note:

"Uncommented mmCIF module because of problems if GNU's Flex is
missing"

because it actually commented it out, not uncommented it! ;) It seems
to me that the setup.py should test whether GNU Flex is there and then
enable the module compilation if it is (as is done for reportlab),
rather than force the user to uncomment sections in the setup.py.  

I would like to enable this functionality in my Fedora package, but as
it currently stands it means that I now need to write a patch in my
RPM to uncomment the stanzas.

Alex