[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.


Eric, we need two things:

(1) The flex binary to convert our lex file into C, which as you point out we might be able to do in advance (assuming this version of flex is unimportant). Detecting the flex binary is pretty easy on Unix like platforms. See comment 4.

(2) The flex headers to compile the C code. This can probably be solved, perhaps looking at similar issues in NumPy.

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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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