[BioPython] PDB parser

[Jeffrey Chang]

Biopython's missing a PDB parser right now, so anything you have would
probably be useful to someone.  :)

One way to speed it up would be to have it output Martel expressions.
I don't know how large of a change that will be to the code, but
Martel is quite fast.  The end user can choose which parts of the file
she wants to receive, which speeds things up by reducing python function
calls.

Jeff


On Mon, Apr 22, 2002 at 11:27:36AM -0400, Michael George Lerner wrote:
> 
> I don't know about other such projects (official or not), but I'm working
> on a PDB parser.  Like Andrew Dalke's UPDB, it reads in format definition
> files and spits out parsers.  Mine uses biopython's Consumer/Parser model
> (I think that didn't exist when Andrew Dalke wrote UPDB).  It seems to
> work fairly well, except for the fact that it's really slow.  Once I can
> speed it up a bit, I'm planning on giving it back to biopython.  Actually,
> I suppose I'll give it back to biopython either way .. but people are more
> likely to actually _want_ it if it runs at a reasonable speed :).
> 
> I guess this message should provide some more motivation for me to get
> back to work on my PDB parser ..
> 
> -michael
> 
> p.s. writing this thing has been a lot of fun.
> 
> --
> This isn't a democracy;|                        _  |Michael Lerner
>  it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
> -Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
>                        |                       / \ | mlerner@umich
> 
> On Mon, 22 Apr 2002, Catherine Letondal wrote:
> 
> >
> > Hi,
> >
> > I have found a link to a PDB parser in a previous message in this
> > archive:
> > http://www.biopython.org/pipermail/biopython/1999-September/000038.html
> > (giving the location of a parser written by A. Dalke) I have tried it
> > and I found it useful, but, since the message is from sept 1999 and
> > Bio/PDB is almost empty, I would like to know whether it's the official
> > one, or whether there are other such projects?
> >
> > Thanks a lot!
> >
> > --
> > Catherine Letondal -- Pasteur Institute Computing Center
> > _______________________________________________
> > BioPython mailing list  -  BioPython@biopython.org
> > http://biopython.org/mailman/listinfo/biopython
> >
> 
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