[Biopython-dev] [Biopython - Bug #2619] Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py

[redmine at redmine.open-bio.org]

Issue #2619 has been updated by Peter Cock.


There was a discussion about this some time ago on our dev mailing list, the consensus as I recall was to aim for a pure Python implementation. That should allow use to support Windows easily, but also support Jython and PyPy, and make supporting Python 3 fairly simple too (have a look at Bio/SeqIO/SffIO.py for and example of a binary parser that works on Python 2 and 3, the only hard bit is explicit bytes vs unicode).

If you would like to work on this, that would be great. I'd suggest a branch on github - but please sign up to the biopython-dev mailing list too. Thanks.
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Bug #2619: Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py
https://redmine.open-bio.org/issues/2619

Author: Chris Oldfield
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 1.48
URL: 


MMCIFParser is a documented feature of Bio.PDB, but it is broken by default because the MMCIFlex build is commented out in the distribution setup.py.  According to  

http://osdir.com/ml/python.bio.devel/2006-02/msg00038.html

this is because it doesn't compile on Windows.  Though the function is documented, the changes need to enable are not, so this seems like an installation bug to me.

The fix on linux is to uncomment setup.py lines 486 on.  A general work around might be to condition the compile on the os.sys.platform variable. I'd offer a diff, but I'm new to biopython and python in general, so please forgive my ignorance.

Source install of version 1.48, gentoo linux 2008, x86_64.


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