[Biopython-dev] flex, setup.py and Bio.PDB.mmCIF (Bug 2619)

Michiel de Hoon mjldehoon at yahoo.com
Wed Feb 6 08:36:26 UTC 2013

Hi Lenna,

Thanks for your reply.
Are you planning to continue your work on the PLY-based mmCIF parser?


--- On Tue, 2/5/13, Lenna Peterson <arklenna at gmail.com> wrote:

From: Lenna Peterson <arklenna at gmail.com>
Subject: Re: [Biopython-dev] flex, setup.py and Bio.PDB.mmCIF (Bug 2619)
To: "Michiel de Hoon" <mjldehoon at yahoo.com>
Cc: "BioPython-Dev Mailing List" <biopython-dev at biopython.org>
Date: Tuesday, February 5, 2013, 8:31 PM

Hi Michiel, 
I worked on that a bit early last year. See thread on this bug: 

Namely, I determined that the flex headers aren't required to compile the flex-generated C, which is a great start. 
I also started work on a PLY-based pure Python reimplementation. Pull request here:


I haven't looked at this code in quite a long time! Let me know if you have any questions about what I did and I will do my best to remember...


On Tue, Feb 5, 2013 at 8:07 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

With Biopython 1.61 now out, perhaps this is a good time to tackle Bio.PDB.mmCIF? This module uses flex to generate the parser; I would like to replace this with a plain C module, or perhaps with a pure-Python parser. This issue was previously discussed here:


Or is anybody else already looking at this module?




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