From chemistry-request@ccl.net Tue May 11 01:20:17 2004
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Message-ID: <40A071C1.4010305<<at>>informatik.uni-tuebingen.de>
Date: Tue, 11 May 2004 08:25:05 +0200
From: "Joerg K. Wegner" <wegnerj<<at>>informatik.uni-tuebingen.de>
Organization: Department of Computer Architecture
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To: Mark Mackey <m.mackey<<at>>cresset-bmd.com>
Cc: chemistry<<at>>ccl.net
Subject: Re: CCL:Enumeration / SMILES handling software
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Hi Mark,

i know only three 'usable' free appraoches:
1. CACTVS from W.D.Ihlenfeld (tcl, no source code for a low price), but 
maybe the best free tool out there.
http://www2.ccc.uni-erlangen.de/software/cactvs/

2. CDK: SMILES with 2D generation
http://sourceforge.net/projects/cdk/

3. JOELib: SMILES and interface to CDK (2D) and Ghemical (3D, simple all
atom force field)
joelib.sf.net

Interesting commercial approaches are:
- 2D: a new tool of Rarey et al.
http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci049958u
- 3D: OMEGA with OEChem as chemistry kernel (formerly called OELib) 
http://www.eyesopen.com/
So they have a good and advanced chemistry and computer science design 
(C++, object oriented, source code available, if you pay for their work).

- 2D: http://www.chemaxon.com/marvin/ (good programming interface)
- 3D: MOE for energy minimization (MMFF94 all-atom pair force field) in 
batch mode
http://www.chemcomp.com/

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:wegnerj<<at>>informatik.uni-tuebingen.de
WWW:    http://www-ra.informatik.uni-tuebingen.de
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