Subject: CCL:file formats/mol. medels; was:V3000 molfile format

From: [email-masked]
Date: Fri, 6 Dec 2002 13:56:36 +0100

To: [email-masked]
Subj: CCL:file formats/mol. medels; was:V3000 molfile format

A public discussion in this list should be nice, and standards may
emerge from it. I do not believe that an universal format is possible
(too many situations), and the molecular models should be defined
before specifying any practical format.
Being a user, the first requirement that I propose is to define
one or several parameters specifying which kind of information
follows (including a release parameter). Then, a set a models
should be defined: chemical graph only, 3D only, chemical graph
plus one or more 3D, and so on... A list of widely accepted
bond types should be welcome. Some other problems: unknown atoms
or bond types, free sites for connectivity, Markush (i.e. generic)
formulas for reactions or patents, superatoms, polymers (how
many units), alloys, coefficients for components, and so on
(there are indeed much more complicated situations).
It is clear for me that specialists of chemical data banks are
able to do many useful suggestions in this area. Computational
chemistry and modeling applications have their own requirements,
and there are many others. But nothing will end before beginning.
Last remark: any programmer should be able read and write molecular
formats (think also to read backward in large databases), without having
to pay amounts of euros or dollars to get black box routines provided
by companies (think to the catastrophic situation on Windows PC).

Michel Petitjean,                     Email: [email-masked]
ITODYS (CNRS, UMR 7086)                      [email-masked]
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html

>If anyone would like to engage in a more detailed discussion about this
>issue or anything else connected with chemical structure representation
>please contact me directly at [email-masked].

---

From: Geoff Hutchison <[email-masked]>
Date: Fri, 6 Dec 2002 15:38:35 -0600 (CST)

Yes, chemistry file formats could be quite complicated and right now we
have a lot of formats for specialized tasks. (e.g. ChemDraw or ISIS files
for publication, CIF files for crystal results, PDB files, Molfiles, Sybyl
Mol2, not to mention the slew of computational packages with their own
formats.)

The approach many of us have used in the past is to use translators like
babel to convert from one format to another. Some data, unfortunately,
might be lost, and some might have to be guessed (e.g. perception of bonds
> from an XYZ file).

> by companies (think to the catastrophic situation on Windows PC).

This is exactly the point of projects like Open Babel. Read and write as
many formats as possible with as little data loss as possible.
<http://openbabel.sourceforge.net/>
(Disclaimer, I'm a developer for OB. It's still a work in progress, but
 improving rapidly.)

Unfortunately, some file formats are entirely black boxes, completely
without documentation. Not much can be done here unless there's enough
pressure on companies to open their formats. Some, like MDL, have open
standards, and this is wonderful. The rest either require reverse
engineering or customer support/feedback to do open their formats.

(IMHO, I think documented formats is entirely in the spirit of sharing
scientific information.)

I don't know if it's "impossible" to have one unified chemical file
format, but it would certainly need to be very flexible. That's certainly
the aim of CML, which may not be "perfect" yet, but seems quite useful.

<http://www.xml-cml.org/>

Just my $0.02,
-Geoff

--
-Geoff Hutchison		<[email-masked]>
Marks/Ratner Groups		(847) 491-3295
Northwestern Chemistry		<http://www.chem.northwestern.edu>

On Fri, 6 Dec 2002 [email-masked] wrote:

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