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

[Lenna Peterson]

Hi Michiel,

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<http://mc/compose?to=mjldehoon@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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