[BioPython] Fwd: bio.pdb.mmcif does not exist

[Jean Lechner]

Hum I ve uncommented the lines and reinstalled all.
But the problem stay the same.
The directory Bio.PDB.mmCIF il here and there is a file named
MMCIFlex.so into it
But python can not load it... it is said that there is no module named
mmCIF.MMCIFlex
so i don t know what to do now ...
If you know answer me please

Jean

2007/5/9, Alex Lancaster <alexl at users.sourceforge.net>:
> >>>>> "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
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