[Biojava-dev] fetching obsolete/superseding files

[Andreas Prlic]

Hi Amr,

> During my research, I met some difficulty in automatically fetching some old
> obsolete files.

ok. May I ask, how did you come across them?


> And that inspired me an idea
> I am thinking in adding 2 new features to the Biojava "structure" module:

Interesting idea. In terms of software design I would not rely on the
parser for this. The local file that is parsed might be already out of
date as well. I would try to keep the parser agnostic of particular
versions or IDs. Instead I would provide a utility class that can give
information on the status of a file. There is a little XML service at
http://www.rcsb.org/pdb/software/rest.do#releaseStatus that provides
the latest status information. That one could be used to fetch the
information and then download any newer (or obsoleted) files...

What do you think?

Andreas

> Supposing that there are 2 new boolean parameters of the PDB file
> reader/Parser which are
> <fetchOboslete> and <fetchSuperseding>
> The first one enables the reader to download a file from the "Obsolete"
> archive if it wasn't found in the main repository;
> while the later searches the header of a file (not necessarily the same
> one) for its newest revision or a superseding new file, fetches it, and
> switch to that new file automatically.
>
> Adding these parameters will need
> 1) Manipulate the URL a little, to enable connecting
> to ftp://ftp.wwpdb.org/pub/pdb/data/structures/obsoleteparsing
> 2) Parsing the OBSLTE, REVDAT, SPRSDE records; as well as REMARK 4, and
> REMARK 5
>
> If these features are approved, I can do them.
>
> Any ideas or comments?
>
>
>
> Amr



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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