Subject: re: CML is dead

From: "E.L. Willighagen" <[email-masked]>
Date: Wed, 12 Apr 2000 00:20:18 +0200 (MET DST)

> I realize that there is a need for (web) publishing tools,
> and that the current java tools are a means to this end, however
> without programs that generate CML there is nothing to publish.
 
1. web publishing is *very* important... note that many ecommerce is
   based in web technology...
2. generation is not that big a problem... several formats can be
   translated into CML (mopac, gaussian, pdb, xyz, mdl-mol to give
   a short list). Combined with the (standard desktop) tool Babel,
   you can transform almost any information automatically into
   CML... and information in *any* format can be generated by all
   software...

So i disagree, that generation of CML data is the problem. A second
thing though is the availability of CML data. And i think in the
"Dutch Dictionary on Organic Chemistry" (http://www.sci.kun.nl/woc/)
we do a fine job in providing "OpenSource" CML data, which consists
mostly of 2D/3D coordinates, but also a growing list of animations
(with energies for each frame).

Moreover, without proper tools to view/use CML data, there is no use
in generating CML data...

But oke, this is maybe what we in the Netherlands call "het kip en
het ei probleem"... (translated: what came earlier: the chicken or the egg)

And i think with these new XSLT stylesheets (see H.Rzepa email) the CML
community is doing a very good job in making CML usefull...

All these effords are a bit inmature now, but will evolve rapidly in the
next year... (i'll promise you that...)

But one thing we certainly *DO* need, is a day-by-day up-to-date website
where every CML tool/application is mentioned...

Finally, we now have a tool to check to validity of CML tools/software
which is a very good thing.

Egon

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From: David van der Spoel <[email-masked]>
Date: Sun, 9 Jul 2000 09:20:34 +0200 (CEST)

>   based in web technology...
Yes but we're talking science here. 

>   CML... and information in *any* format can be generated by all
I don't want babel! I want native support by *all* chemistry applications.
That's right *all* applications! I realize that is a tad optimistic,
especially considering that we have already lost Schrodingers support. But
if that is not the aim, CML is just another file format. Users don't want
to keep track of N versions of the same data, just because their N
different applications need a reformatted version of this data. Even if
you can convert with babel, this is still extremely messy. 

>in generating CML data...
That's why someone has to bite the bullet and write the library, and then
implement it in some of the leading packages, like rasmol and xmgrace.
I keep hammering on those two programs, because those are the most
important ones!

>next year... (i'll promise you that...)
There is no sign of evolution in the direction that I pointed out. 

>which is a very good thing.
I agree to this, and moreover I don't want to suggest that the current
tools are useless. However I think what the average user wants is her/his
program to generate data that she/he can load into another analysis
program immediately. If one could also use the data in a web presentation
that would be a big plus. 

What needs to be done is probably to involve organisations like ACS and
others, and have them bless CML as the standard of chemical information.
Looking on the ACS website I found that CML is already being accepted for
electronic submission of two ACS journals, which is promising in this
respect.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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From: Gerald Loeffler <[email-masked]>
Date: Wed, 12 Apr 2000 12:13:55 +0200

okay - I can't resist adding my $0.02:

When talking about XML there are 2 completely separate issues that are
constantly being mixed up here - allow me too to try to clear the matter
a bit:

XML itself just defines the plain general syntax for writing
_conformant_ XML-files (equivalent to saying "we are using
comma-separated text-files") and also provides the means of describing
what a particular _valid_ XML-document must look like (through the DTD,
equivalent to saying "the first column in this comma-separated text-file
is the 3-letter atom-code"). (note: "valid" is stronger than
"conformant"!) So:

1) XML-enabled software must be able to parse (read!) XML-files and
DTDs: parsers for this _are_ available _now_ in all languages that
matter in this context (C (http://www.jclark.com/xml/expat.html, ...),
C++ (http://www.alphaworks.ibm.com/tech/xml4c, ...), Java
(http://www.alphaworks.ibm.com/tech/xml4j, ...), ... no FORTRAN). This
enables the software to read conformant _and_ valid XML-files of any (!)
kind.

2) CML-enabled software must additionally (!) be able to "understand"
the CML-semantics (it must "know" what a 3-letter atom-code means) and
must be willing to write CML-files. This is an additional issue and
different chemistry software packages won't be any more "co-operating"
than now unless all agree to "speak" CML (or any other chemistry-DTD)
(in addition to XML)!

	cheers,
	gerald

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