Subject: SUMMARY: SMILES query

From: Eugene Leitl <[email-masked]>
Date: Sat, 5 Jun 1999 23:08:04 -0700 (PDT)

This is the summary of the answers I got for my query on resources for
(U)SMILES ( http://www.daylight.com/dayhtml/doc/theory/theory.toc.html ) 
generation and manipulation. 

It seems that interim Daylight has silently revised the USMILES
(unique SMILES) specs so that currently (1999) ~30% of the free NCI 
database now differs if compared to those produced using the rules
>from the original (1989) publication. Hopefully, in near future either 
the new specs will be published or the generation algorithm reverse-
engineered. 

Thanks to all who contributed.

Regards,
Eugene Leitl

Edited replies follow.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: Peter Bladon <[email-masked]>

I have written software for _parsing_ SMILES strings as a means of structure
input to the INTERCHEM modelling system, and as a general way of generating
3D-structural data. I have not undertaken the generation of unique
SMILES strings, although I am actively considering it. The version of
SMILES I have adopted is the simple one outlined in the original papers by the
Weiningers.  But I have adapted it to take care of conformational and chirality
information to simplify the generation of 3D-structures.  So the
chirality information is specified in a different way to that used in
the current Daylight codes.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: Nick Jewell <[email-masked]>

I use Tripos's dbtranslate facility (comes with the
Unity database package) to convert smiles into MOL or
MOL2 formats. All in all, similar to babel but more
helpfully documented.

For more information on this source, consult
http://www.tripos.com
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: Ferenc Csizmadia <[email-masked]>

Marvin Sketch generates SMILES and SMARTS (an extension of SMILES for
querying) strings and other formats.
See http://www.chemaxon.com/marvin/ for more.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: "Wolf-Dietrich Ihlenfeldt" <[email-masked]>

The CACTVS toolkit does it, too.
http://www2.ccc.uni-erlangen.de/cactvs/

See also our selection of Internet chemistry services
at http://www2.ccc.uni-erlangen.de/services, which generally
accept SMILES as input.

Other programs with SMILES capabilities:
CS ChemDraw, ChemAxon Marvin Java Editor, Novartis JME Java Editor
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: [email-masked]

we are using smiles extensively in our chemical databases (daylight, ORACLE)
as a key for fullstructure search.
There are also a few other Chemical Editors which can create SMILES:
Daylight has one,
there is a free one from Peter Ertl:
http://www.daylight.com/bernd-cgi/Novartis/download.cgi
ChemDraw
others.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: "Pierre-Jean L'Heureux" <[email-masked]>

MOE, a Chemical Computing Group software, does use SMILE for database
searching.

http://www.chemcomp.com/
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