[BioPython] FSSP module: any comments?

[Iddo Friedberg]

Hi all,

In the BM era (Before Martel), or actually in the BIKHTWDP era (before I
knew how to write a decent parser), I wrote a module which parses FSSP
files.

Crowd: (Oh no, another file format! Where are the tomatoes!?)

Not exactly. FSSP stands for Families of Structure Structure aligned
Proteins. It is an automatically updated database, which essentially
partitions PDB into protein families which are structure related. Each
FSSP file is named after a representative protein, to which others are
aligned. Essentially those files contain information in terms of multiple
structual alignment of proteins. Actually, pairwise-multiple, as all the
structures there are aligned to th representative.

More on FSSP here:

http://www2.embl-ebi.ac.uk/dali/fssp/fssp_help.html

The FSSP module parses the Summary and Alignments sections of the file.
The other two, Equivalences and Matrices are not handeled. Yet.

The read_fssp function reads an FSSP file and returns a tuple of a Summary
object and an Alignments object. The Alignments object can be converted to
a Bio.Align.Generic, but there is a loss of secondary structure
information, PDB sequence information, and actually, anything which isn't
pure sequence.

Another function there filters an alignment according to criteria such as
similarity, alignment lenght DALI Zscore (measure of structural
similarity), and so on.


Good thing about it: it appears to be working.

Bad thing: not in Martel, doesn't even look like a decent parser. I do it
all with regexps, but the FSSP format is so well-defined and robust, that
I haven't crashed yet.

Do we need it? Would anyone like to comment?

Iddo

--

Iddo Friedberg                                  | Tel: +972-2-6758647
Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg@cc.huji.ac.il
POB 12272, Jerusalem 91120                      |
Israel                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/