[Bioperl-l] New modules for STRIDE and DSSP output

[Ed Green]

I've just committed two new modules for parseing and accessing
STRIDE and DSSP output.  These
programs examine structures (pdb files) for secondary structural
elements and some other things.

They modules are here:
Bio::Structure::SecStr::DSSP::Res.pm
Bio::Structure::SecStr::STRIDE::Res.pm

Being new to this project, I read the bioperl.org coding conventions and
have tried to conform to them.  I have two questions, though:

1.  How are external dependencies handled / added?
    Currently, these modules use Root::IO to get at the STRIDE or DSSP
output, but they could be enhanced to actually run the programs
themselves (factory-like).  This would add an optional bioperl dependency.

2.  Are there rules for adding examples / tests?
    I've written some example / test scripts which could be helpful to
someone who wants to use these modules.  Is it kosher to just add those
to the examples subdirectory?

Since the Bio::Structure objects are in flux, I have not tried to
integrate with them.  When thay are more settled, there are obvious ways
that these secondary structural objects could be integrated with the
more general structure objects.

And in regard to the new Bio::Structure object, I think it does a good
job capturing and organizing structural info, but may be a bit too heavy
for high-throughput work because of the sheer number of objects created
(1/residue & 1/atom).  I'd like to cast my vote for having an
additional, leaner Bio::Structure object that is (gasp!) less
objectified, but more suitable for high-throughput work.  The idea
of having dual structure objects was first suggested here:

http://www.bioperl.org/Projects/Structure/requirements.html

For those interested, some highlights in the surprisingly long history
of the contemplation of a bioperl structure object are here:

[from 1995]
http://scop.mrc-lmb.cam.ac.uk/pub/bioperl/mlist/maillist.html

and around December 1998 in the bioperl-l list web-archive here.


STRIDE can be found here:
http://www.embl-heidelberg.de/argos/stride/down_stride.html
DSSP can be found here:
http://www.cmbi.kun.nl/swift/dssp/

If you have an "old" version of stride (older than Nov. 29, 2001), you 
need to upgrade to the current version to use that module.

Regards,
Ed Green

-- 
*****************************
Ed Green
Graduate Student - Brenner Research Group
UC Berkeley
510-642-9614
ed@compbio.berkeley.edu
http://compbio.berkeley.edu
*****************************