[Biopython] Mining the PDB header

[Ahmad Abdelzaher]

Sorry for the misunderstanding, but I'm mining the structures
themselves. To be more precise, I'm doing structure prediction
analysis. I'm not doing text mining of the headers themselves. I'm not
sure which classification is used in the PDB, how consistent it
is,...etc. I would be interested in any information regarding the
function, or localization,..etc. If you think I'm not quite sure what
I want, you'd be correct. Ultimately I will be clustering the
structures based on that classification.

On Thu, May 11, 2017 at 8:28 PM, Lenna Peterson
<lenna.peterson at gmail.com> wrote:
> Well, your original question did ask how to mine the PDB header with Python.
>
> "protein classification" is not a specific term (do you mean organism?
> function? fold? etc.) - is this something that appears in the PDB header? If
> so, what PDB header field is it in?
>
> Lenna
>
>
> On Thu, May 11, 2017 at 1:49 PM, Ahmad Abdelzaher <underoath006 at gmail.com>
> wrote:
>>
>> I'm not trying to mine the actual header. I would definitely be
>> interested in an option that retrieves the protein classification
>> without having to write any additional code. Does such option exist?
>>
>> Regards.
>>
>> On Thu, May 11, 2017 at 7:06 AM, João Rodrigues
>> <j.p.g.l.m.rodrigues at gmail.com> wrote:
>> > You can do *some* mining. Look at parse_pdb_header.
>> >
>> > 2017-05-10 18:58 GMT-07:00 Ahmad Abdelzaher <underoath006 at gmail.com>:
>> >>
>> >> Hey guys,
>> >>
>> >> Unfortunately  I read this in the FAQ page:
>> >>
>> >> " If you are interested in data mining the PDB header, you might want
>> >> to look elsewhere because there is only limited support for this."
>> >>
>> >> So if I can't do it with biopython, what other alternatives do I have?
>> >> I'm doing some PDB mining and I'm interested to retrieve the
>> >> classification of the structure, to do some clustering analysis later.
>> >>
>> >> Cheers.
>> >> _______________________________________________
>> >> Biopython mailing list  -  Biopython at mailman.open-bio.org
>> >> http://mailman.open-bio.org/mailman/listinfo/biopython
>> >
>> >
>>
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>
>