[Biopython] Bio.PDB local MMCIF files

[Michiel de Hoon]

OK, I will hold off for now then. -Michiel



------------------------------
On Sat, Dec 28, 2013 3:11 PM EST João Rodrigues wrote:

>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
>>
>>  _______________________________________________
>>  Biopython mailing list  -  Biopython at lists.open-bio.org
>>  http://lists.open-bio.org/mailman/listinfo/biopython
>>
>>