[Biopython-dev] Implementation advice

[Cayte]

I just finished NetCatch.  Seems like it could blend in with NetCatch.py
that I just uploaded. NetCatch takes a dictionary of links and reads in
links selected by the user.  Each value is a file or link but it could be a
list.
Let me know if I can make it more usable.

BTW your python is cute.   But I'd like to  see helical "reticulations" for
its pattern.  After all, its a biopython, not any python.

                                                       Cayte
> Hi all,
>
> I am trying to expand the functionality of FSSP a bit. As part of that, I
> would like to provide the user with the ability to give a PDB id, and
> retrieve the name of the FSSP file(s) containing that PDB id.
>
> Without getting into too much details, each FSSP file (out of some 2800)
> has anywhere between 3 and 300 PDB ids, some of them in more than one
> file.
>
> I was thinking of creating a dictionary which will look something like:
> { '1chyA': ['1xyzB','3fgy0'],
>   '3dcp0': ['3syx'],
>   '2abcC': ['3syx', '4rde'],
> .
> .
> .
> }
> # Meaning, that 1chyA is in the FSSP file represented by 1xyzB and in the
> # one represented by 3fgy0
>
> Dictionary creation will be a one-time thing, its updates as frequently as
> the user likes (not very frequent), and queries will be many (very
> frequent). It seems a bit large to read (some 2800 keys, and rising) in
> anytime you actually need to find out where 2abcC is located, so I thought
> of using the Python dbm interface.
>
> 'anydbm', so as to maximize platform independence.
>
> ***** Is this good so far? Or is there a better tool I can use? I don't
> want to use SQL here... seems a bit of an overkill.
>
> Because anydbm (as do gdbm, dumbdbm...) accepts only strings for keys and
> values, and I'd like to use lists in the values (maybe also in the keys),
> I thought that creating a UserDict instance which overloads __getitem__,
> __setitem__, etc. , using cPickle.loads and cPickle.dumps for key and
> values, this transparently enabling the use of non-strings in a Python dbm
> interface. (Bit of code attached).
>
> **** This seems a very generic application. I'd be extremely surprised if
> nobody did something like this before. But I couldn't really find
> anything. Comments?
>
>
> Thanks,
>
> Iddo
>
>
> --
>
> Iddo Friedberg                                  | Tel: +972-2-6757374
> Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
> The Hebrew University - Hadassah Medical School | email:
idoerg at cc.huji.ac.il
> POB 12272, Jerusalem 91120                      |
> Israel                                          |
> http://bioinfo.md.huji.ac.il/marg/people-home/iddo/
>
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