[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.


Is the desire to use a C parser due to performance concerns (30k+ line files)?

I can think of two cross-platform alternatives to flex. Maybe Windows 9 will be *nix based and we can escape these problems. 

1) There is at least one python implementation of lex: http://www.dabeaz.com/ply/ (BSD license)

2) The mmCIF parser could possibly be written in core python. There's a perl CIF parser: http://pdb.sdsc.edu/STAR/index.html (UCSD license)

I don't have experience with lexical analysis, but it seems like cross-platform support for CIF is important. In which direction would my efforts be best directed? 
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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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