[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 Lenna Peterson.


I've been reading about flex and found the following line in the book "flex & bison" (John Levine, O'Reilly):

> Most flex programs now use @ %option noyywrap @ and provide their own main routine, so they don’t need the flex library.

This suggests the flex headers aren't absolutely required for the C module, which would make *nix detection possible. I'll look into this. 

Also, I have a prototype with PLY that works fine for small files but doesn't parse a full 30k line CIF file in an acceptable time. 
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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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