Subject: Re: CCL:XML as program output?

From: Konrad Hinsen <[email-masked]>
Date: Wed, 19 May 1999 14:39:51 +0200

On Tue, 18 May 1999, David E. Bernholdt wrote:

> You run a chemistry code -- say an SCF calculation, to be concrete.
> Would you prefer that the primary output of this program be in plain
> text, as nearly all packages I'm familiar with now produce, or would
> you prefer it to be thoroughly marked-up XML?

Both. I'd want a brief calculation protocol as text, to let me
check quickly if everything looks right. But I'd want detailed results
in a machine-readable format. And there XML has many advantages.

> How about if the XML conformed to a standardized schema that was used
> by _all_ SCF programs, so that they all marked up their output the

That's of course every user's dream, but why should program developers
suddenly become able to agree on standardized data formats? That
sounds overly optimistic to me. I can't think of any data which is
not either proprietary or insufficient!

On the other hand, even with dozens of proprietary DTDs, standardizing
on XML would be an advantage. All files could be fed to one and the
same parser, and the fact that XML files are human-readable text files
already guarantees some basic intelligibility.

On Tue, 18 May 1999, David van der Spoel wrote:

> chance at all to be accepted as "standard" I think the following demands
> have to be met:
> - Chemistry/XML format should be non proprietary, i.e. it may not be
>   crippled by browser vendors (like HTML). Ideally the format should be
>   controlled by chemists

Someone will have to define one or more DTDs for chemistry, and
designing DTDs is not a trivial job. If this job is left to companies
(or also program authors in academia), there will probably be
incompatible proprietary DTDs. If it is left to people who are not
program authors, the result might be insufficient for practical use.
And if it is left to some committee, it will take decades to reach a
bad compromise.

> - There should be a free (GPL'ed) library which programmers can use to
>   write xml output (callable from at least C and fortran, meaning that it
>   should *not* be a C++ library).

Writing XML is very easy and hardly needs support libraries. The
difficult part is *parsing* XML, but there are already a few parsers
around.

> - There need to be fast portable browsers

These will probably be provided by non-chemistry people, but it remains
to be seen if they will be flexible enough to permit the addition of
features such as chemical structure visualization.
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From: Gerardo González Aguilar <[email-masked]>
Date: Wed, 19 May 1999 08:24:42 -0400 (CDT)

Hi all!

My point of view is that a unified program output is a great idea, is very
simple to work with it and to implement pipelines from one program to
another, the principal problem will be related with their implementation
in the standard packages actually used, but the effort to rewrite the code
for these programs is llttle compared with the advantaged of a unified
code and finally it make unnecessary translators as Babel that cannot
fullfill the requirements of all people who need to do somw works with
different packages 

Bye.

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                   |                        | e-mail:
Gerardo Gonzalez   |  Dpto. de Quimica      | [email-masked]
Prof. of Chemistry |  Univ. de Camaguey     | or:
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                   |  Camaguey 74650, Cuba  |
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