[Biojava-dev] fetching obsolete/superseding files

[Amr AL-Hossary]

Dear Dr. Andreas,

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

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

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