Subject: Re: CCL:2D pictures/structure generator

From: Christoph Steinbeck <[email-masked]>
Date: Fri, 27 Sep 2002 11:48:08 +0200

Iain Wallace wrote:
> Hi all,
>  
> I have two quick questions if you don't mind:
> 1) Does any one know of a free program that convert molecules in smiles 
> format ( or some other format) into a picture, using a command line for 
> windows. I want to create an excel spreadsheet with a picture of each of 
> my molecules, by using a simple script.
> 2) Does any one know of a free program that can generate molecules based 
> on a given fragment. I have a drug molecule, and a protein, and would 
> like to generate molecules by modifying some of the substituents of the 
> drug molecule and attempt to dock them.
>  
> Thanks for any help you can give me
>  
> Iain
>  

Please try our Chemistry Development Kit (CDK), a free Java toolkit for 
structural chemo- and bioinformatics. It is available from 
http://cdk.sourceforge.net

The CDK provides methods for parsing SMILES and creating coordinates for 
the molecule by structure diagram layout. Output in a common graphics 
format can then be done using the BATIK toolkit.

I guess, that is as close as you can get to solving your problem with 
free software.

Admittedly, there is no command line wrapper for this, but that would be 
just 5 to 10 lines of code.

The CDK also contains some stochastic structure generators but they 
might not be easily adapted to your problem, because they are isomer 
generators, which only produce isomers of a given molecular formula.

Cheers,

Chris

-- 
Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf)
MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 
Jena, Germany
Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

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From: Jamie Platts <[email-masked]>
Date: Fri, 27 Sep 2002 09:07:33 +0100 (BST)

Hi Iain - take a look at Daylight's Depict utility:

http://www.daylight.com/daycgi/depict

where you should be able to save the generated structure as a GIF. Hope
that helps,

  Jamie