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

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Sat Apr 21 10:39:15 UTC 2012

Issue #2619 has been updated by Peter Cock.

Status changed from New to Closed
% Done changed from 0 to 100

Fixed with Lenna's work - see this commit and its parents:
Bug #2619: Bio.PDB.MMCIFParser component MMCIFlex commented out in setup.py

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

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  


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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