Structure conversion software

Robert Shell Robert at Asheep.Demon.CO.Uk
Sun Feb 4 18:09:44 EST 1996


philippe at ICPL2.UNIV-LILLE2.FR (Philippe CHAVATTE) wrote:

>>I look for a software which can convert structures 2D or 3D in SMILES chemical
>>notation line.

There are a large number of methods for handling the convertion of between 1D line
notations like SMILES , 2D depictions for papers and documents and 3D molecular
configurations for modelling and property calculations. One of the best source of
these utilitiies is the Daylight with their Programming tool-kits and applications.

For quick creation of 3D configurations for 3D chemical database searching and
starting points for MOPAC and other calculations are are a number of commerical tools
:-

Concord 	Tripos USA 
Rubicon 	Daylight see http://www.daylight.com
Chem-X		Chemical Design limited UK

CACTVS               see http://schiele.organik.uni-erlangen.de/cactvs
		(free convertion service for a small number of structures via the WWW)

There creation of smiles codes from 2D depictions is handled by ChemDraw, ChemWindows
and many other chemical drawing programme. There CACTVS system contains a good free
graphical editor for creations of smiles on some common unix platforms.
The ability to convertion of Smiles to 2D depictions is less common. There Daylight
WWW page http://www.daylight.com provides a simple Web page for this. The following
tools are also available for the PC environment.

Consisant	Exographics USA
Accord		Synopics UK
Unity		Tripos USA
Depict-Toolkit	Daylight

The Best utility I have found for the general conversion between the various 2D
formats Babel released by the Dept. of Chemistry, University of Arizona,Tucson, AZ
85721	babel at mercury.aichem.arizona.edu	(source code is available)

Yours Robert Shell

Research Computing, 
Dagenham Research Centre 
Rhone Poulenc Rorer UK





More information about the Bio-soft mailing list