[BioPython] PDB handling package

Andrew Dalke dalke@bioreason.com
Thu, 16 Sep 1999 12:04:10 -0600

Iddo Friedberg <idoerg@cc.huji.ac.il>
> I've been fitting my PDB (Protein Data Bank) file handling
> package for public consumption

That reminds me, there is a similar program I worked on last
year called UPDB which is a parser generator for PDB files.
It reads the PDB format specifications and generation PDB
parsers for Python, Perl and Tcl.

It supports all of the card types I could find, in both
v1 and v2 PDB formats, as well as several variations I know

Here's one of the original announcements with a bit more information.


I haven't had the time to finish it off, but the code is available
from ftp://ftp.ks.uiuc.edu/pub/group/dalke/UPDB-0.5.tar.gz .
Several other people have gotten it to work, but it isn't in a
directly useful state.

Still, it does parse many more cards than your PyStruct class
does, and deals with, eg, changes in the ATOM card definition
over time (your code won't deal with pre-segID records or records
with the line number in the last columns -- reflecting the PDB's
FORTRAN heritage!).  So you might want to take a look at it.

OTOH, it doesn't try to deal with anything other than parsing
lines from a PDB file, while you code has analysis functionality.

						Andrew Dalke