Subject: Re: CCL:Compressed PDB list.

From: [email-masked] (Pieter Stouten)
Date: Fri, 27 Oct 1995 13:50:24 -0400

At 8:16 95/10/27, Ernest Chamot <[email-masked]> wrote:

>Oxford Molecular went through the PDB database, making it consistent
>and fixing up irregularities.  They now offer it as relational database
>called Iditis,
>
I always wondered why they would use a relational database paradigm.
Proteins are ordered and the information one wants to retrieve often
involves stretches of residues with certain characteristics. Using a
relational database, one needs to do many operations. It seems to me that a
mixture of pattern matching (with additional bonus of easily allowing for a
few mismatches) and relational operations would be much more efficient.
Does anybody have any opinions about this?

Thanks, Pieter.

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From: Eugene Leitl <[email-masked]>
Date: Fri, 27 Oct 1995 21:35:38 +0100 (MET)

> Does anybody have any opinions about this?

I think there are at least two C++ libraries (PD) which put an OO
abstraction layer upon the ugly flat ASCII pdb file structure (which,
horrors! isn't even formally defined). I can look up the names and the 
pointers to them, if needed. Apropos OO, wouldn't a true OO dbase (such 
as Poet, which knows persistant C++ objects) come quite handy as a pdb 
object container?

-- Eugene
 
[ tail snipped for the bandwidth's sake ]

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From: [email-masked] (Hinsen Konrad)
Date: Fri, 27 Oct 1995 21:58:53 -0400

I have been using pdb++ for a while, which does what it claims to
do. However, that means "just" I/O - basically it provides input and
output streams for C++ where each object read from the stream or
written to the stream corresponds to one line in a PDB file. So it
doesn't really do anything about the flat file structure, but it does
handle the nasty details of handling Fortran-style fixed format files
from C++.

Certainly. But all OO data bases I know of are very proprietary and
available only for a limited number of systems (and expensive, of
course). Poet is a good example.

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