[Bioperl-l] Some code that might be useful for bioperl (fwd)

[Jesus M. Castagnetto]

Ewan Birney, suggested I forward this email to the list.

Hope is useful.

--
Jesus M. Castagnetto <jesusmc@scripps.edu> - "Ken Zen Ichi-nyo"
Program Project:   http://www.scripps.edu/research/metallo/ 
Metalloprotein DB: http://metallo.scripps.edu/
PalmPilot Stuff: http://www.geocities.com/jm_castagnetto/

---------- Forwarded message ----------
Date: Fri, 23 Feb 2001 20:23:42 -0800 (PST)
From: "Jesus M. Castagnetto" <jesusmc@crystal.scripps.edu>
To: birney@sanger.ac.uk
Subject: Some code that might be useful for bioperl

Hi,

Just found bioperl, while looking for bioinformatics and xml
info on google. Saw that you are planning on doing some 3D
structure representation coding, and I have some code, but
it is not in Perl. It is in PHP, which is close enough, so
you could just modify it w/o much trouble.

Wrote if for my own use for the MDB (metallo.scripps.edu),
and a couple of days ago I tested the simple PDBParser class
(more info below) to go over our local copy of the PDB
(about 14,500) in about 13 hours, extracting all HIS
(w/ some cheating by using grep :) and calculating chi-angles
and putting them into a db (see chi_crawler.php in Chem/test).

You can see the documentation, made w/ phpDoc -a program that
is still being developed by its author, so some prototypes are 
mangled-, at the URL:

	www.castagnetto.org/Chem/index.html

and you can get the classes from:

	www.castagnetto.org/Chem/Chem.tar.gz

Basically they are classes defining base Atom, Molecule and 
Macromolecule objects, with some PDB derivated classes, and a
couple of PDB parsing classes, a PDBFile which can have one
or more macromolecules, and is really object heavy, and a
stand-alone simple PDBParser class. Nothing fancy, just some
utility classes.

My use of Perl is very basic. I use PHP, Java and Python more
often, but if you got a question/suggestion about the classes
I'll be happy to try to help/implement changes.

Regards.

--
Jesus M. Castagnetto <jesusmc@scripps.edu> - "Ken Zen Ichi-nyo"
Program Project:   http://www.scripps.edu/research/metallo/ 
Metalloprotein DB: http://metallo.scripps.edu/
PalmPilot Stuff: http://www.geocities.com/jm_castagnetto/