[Biopython] Bio.PDB local MMCIF files

[João Rodrigues]

Dear all,

I agree that the code for mmcif parsing should be improved. However, I also
think that we should move to an entirely new module to have sane names.

The people at the EBI-EMBL have developed an efficient and robust mmcif
parser that they would like to share with us so we can integrate in our
code.

I'm currently on holidays, I'll be back to work in a couple of weeks, so I
suggest we postpone this discussion until then?

Cheers,
João
Em 28/12/2013 02:10, "Michiel de Hoon" <mjldehoon at yahoo.com> escreveu:

> Various issues of the MMCIF parser also came up previously, see for
> example the thread starting here:
>
> http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010452.html
>
> I'd like to propose to make the MMCIF parser a bit more Pythonic and more
> consistent with other Biopython modules.
> This is a description of how the MMCIF parser would work:
>
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.mmcif_proposal.html#htoc149
>
> This uses a new Bio.PDB.mmcif module that has a read() function (taking
> both file names and file handles) which stores the information in an MMCIF
> file in a mmcif.Record object, which is a Python dictionary.
>
> Please have a look if you agree or have any comments or suggestions. If
> this looks OK, I can upload the new code.
>
> Best,
> -Michiel.
>
> --------------------------------------------
> On Thu, 12/5/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>  Subject: Re: [Biopython] Bio.PDB local MMCIF files
>  To: "João Rodrigues" <anaryin at gmail.com>
>  Cc: "Biopython Mailing List" <biopython at lists.open-bio.org>
>  Date: Thursday, December 5, 2013, 12:35 PM
>
>  On Thu, Dec 5, 2013 at 4:53 PM, João
>  Rodrigues <anaryin at gmail.com>
>  wrote:
>  > Hi Dave,
>  >
>  > I understand your concern. Python has the gzip module
>  that can decompress
>  > the files on the file and provide a handle for the
>  content. This will not
>  > work for the parsers since they except a filename. I
>  will have a look at
>  > the parsers code and if it's simple, I'll add a layer
>  to do this exactly.
>  >
>  > Cheers,
>  >
>  > João
>
>  Yeah, most of Biopython's parsers take a handle only, some
>  like the top level functions in Bio.SeqIO, AlignIO,
>  SearchIO
>  will take a filename or a handle for convenience.
>
>  I agree that is is unfortunate that Bio.PDB currently only
>  takes
>  a filename (historical design choice). If we can tweak it to
>  take
>  either a filename or a handle that would be much better :)
>
>  Regards,
>
>  Peter
>
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