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

[Michiel de Hoon]

Hi Lenna,

--- On Thu, 2/7/13, Lenna Peterson <arklenna at gmail.com> wrote:
> If
 there are well-defined problems with the PLY parser, I can work on
> fixing them. I am not currently working with mmCIF so I am not in the
> best position to evaluate where and how the parser needs to be improved.
 




I don't know of any problems with the PLY parser, but since it relies on PLY, it would add another dependency to Biopython. On the other hand, a pure-Python solution may be preferable, as it's easier to maintain and runs with Jython. The C implementation is considerably faster, but I doubt that it really matters since the Python (PLY) parser seems to be fast enough.

I see three options then:
1) Remove the lex stuff from lex.yy.c, and optionally convert the remaining C code to Python.
2) Remove the PLY dependency from the PLY-based parser.
3) Write a new pure-Python parser from scratch.

I'm guessing that 1) will be the most straightforward. Other opinions?

Best,
-Michiel.


--- On Thu, 2/7/13, Lenna Peterson <arklenna at gmail.com> wrote:
If there are well-defined problems with the PLY parser, I can work on fixing them. I am not currently working with mmCIF so I am not in the best position to evaluate where and how the parser needs to be improved. 


I am working with X-ray PDB files and I am not sure if my collaborators are familiar with mmCIF. I have not dealt with NMR files of any type, either. 
Cheers,

Lenna

On Wed, Feb 6, 2013 at 3:36 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

Hi Lenna,

Thanks for your reply.

Are you planning to continue your work on the PLY-based mmCIF parser?

Best,
-Michiel

--- 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: 
https://redmine.open-bio.org/issues/2619



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:



https://github.com/biopython/biopython/pull/33

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...



Cheers,
Lenna

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:






http://lists.open-bio.org/pipermail/biopython-dev/2008-October/004466.html



Or is anybody else already looking at this module?



Best,

-Michiel.

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