Subject: Re: CCL:smiles to sdf converter

From: George Vacek <vacek!at!eyesopen.com>
Date: Wed, 01 Dec 2004 11:52:01 -0700

> I am looking for a smiles to sdf converter able to run on PC/Win.

What do you mean by SMI to SDF conversion?  For what purpose?

You can use the babel2 script that is shipped with the OEChem Toolkit to 
make the direct conversion.  The information will be put into the right 
format, but the coordinates will be 0.00 because SMI actually doesn't 
have any coordinate information.  [Matt Stahl, who wrote Babel with Pat 
Walters, is one of the authors of OEChem].

You can use OGHAM to convert SMI into 2D coordinates suitable for 
depiction (and also do the depictions).

If you want to generate 3D coordinates check out OMEGA, which will 
generate full conformational ensembles.

All of our software runs on a multitude of platforms, including Windows. 
  More information on all three is at http://www.eyesopen.com/products/

It's not clear from your signature where you are working, but for 
non-commercial use, all OpenEye software is available at no charge.

Regards,
George Vacek

VP, Business Development
OpenEye Scientific Software
vacek!at!eyesopen.com
505.473.7385

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From: Egon Willighagen <e.willighagen<<at>>science.ru.nl>
Date: Wed, 1 Dec 2004 20:08:29 +0100

On Wednesday 01 December 2004 16:57, Jiri Krechl wrote:
> Apparently Babel might be the solution but the last version I could found
> for DOS environment (babel16) does not seem to support smiles among
> otherwise wide variety of input/output formats.

A few opensource options:

OpenBabel: http://openbabel.sf.net/
JOELib: http://joelib.sf.net/
Chemistry Development Kit: http://cdk.sf.net/

kind regards,

Egon

-- 
e.willighagen<<at>>science.ru.nl
PhD student on Molecular Representation in Chemometrics
Radboud University Nijmegen
http://www.cac.science.ru.nl/people/egonw/
GPG: 1024D/D6336BA6

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From: Eric Bennett <ericb*at*POBOX.COM>
Date: Wed, 01 Dec 2004 13:08:52 -0600

Jiri Krechl wrote:

>I am looking for a smiles to sdf converter able to run on PC/Win. Apparently
>Babel might be the solution but the last version I could found for DOS
>environment (babel16) does not seem to support smiles among otherwise wide
>variety of input/output formats.
>
>  
>
There is a more recent precompiled Windows version of Open Babel 
(successor to Babel) here:
http://cml.sourceforge.net/new/

OpenBabel sort of supports SMILES but according to the docs it sets all 
the atom coordinates to zero instead of trying to build a reasonable 3D 
geometry, so it may or may not fit your needs.

-- 
Eric Bennett, Center for Drug Design, U of Minnesota

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From: "M. Nicklaus" <mn1(at)helix.nih.gov>
Date: Wed, 1 Dec 2004 16:39:33 -0500 (Eastern Standard Time)

Jiri,

> variety of input/output formats.

If something that can be run *from* a PC instead of *on* one would be of
use to you, you can use our web service at
http://cactus.nci.nih.gov/services/translate/.  You can submit text files
with multiple SMILES strings, and you can choose between 2D and 3D
coordinates in the generated SD file.

Hope this helps,

Marc

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 Fax:    (301) 846-6033                  FREDERICK, MD 21702      USA
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