[Molecularmechanics] Re: Re: Some general remarks.

[Eugen Leitl]

--8jEihaNHb65WmIJG
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
Content-Transfer-Encoding: quoted-printable

On Mon, Nov 24, 2003 at 11:02:33AM +0100, Konrad Hinsen wrote:

> All I know is smiles, which I think is not sufficient for our needs, and=
=20

Unique SMILES are a normalized format. They're like a hash of a molecule,
except that there are no collisions. They're compact, being a single line
of text, and can be cut & pasted into email, or listed in text files
one molecule/line.

They don't have 3D coordinates, though, and there's no standard
open source code to generate good-quality *standard* 3D coordinates=20
from SMILES.

> difficult to build on. Smiles represents only the elements and the bond=
=20
> structure in between them. There is no way to attach any other informatio=
n,=20
> not even unique atom names to which one could refer from elsewhere. There=
=20
> isn't any support for intra- or supramolecular structure either. From wha=
t I=20
> could find about IChi, it seems to have similar aims as smiles, so I expe=
ct=20
> it to have similar shortcomings for specifying simulation systems.
>=20
> What I like about XML-based formats is their extensibility, it is always=
=20
> possible to add on more information in such a way that programs that don'=
t=20
> need it can just ignore it. I think this is important in a field that is=
=20
> still rapidly evolving.

I think SMILES can't be included in XML without armoring.
=20
-- Eugen* Leitl <a href=3D"http://leitl.org">leitl</a>
______________________________________________________________
ICBM: 48.07078, 11.61144            http://www.leitl.org
8B29F6BE: 099D 78BA 2FD3 B014 B08A  7779 75B0 2443 8B29 F6BE
http://moleculardevices.org         http://nanomachines.net

--8jEihaNHb65WmIJG
Content-Type: application/pgp-signature
Content-Disposition: inline

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.2.2-rc1-SuSE (GNU/Linux)

iD8DBQE/weFadbAkQ4sp9r4RArxWAJ4hjMCBBT7RFW+V1gz3JyH9SUo6EQCgohaD
sB3/lnv0IcEf3XctcgHW7io=
=J3oR
-----END PGP SIGNATURE-----

--8jEihaNHb65WmIJG--