Subject: 3D->2D softwares?

From: "JunJun Liu" <ljjlp03/at/gmail.com>
Date: Mon, 27 Jun 2005 15:56:15 +0800

Dear All:

Is there a software in linux can convert 3D small organic structures to 2D
sketch structures? It will be more preferable if the software has a
function of exporting 2D structures to picutures. Thanks in advance!

Liu

-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China

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From: "Noel O'Boyle" <noel.oboyle2_at_mail.dcu.ie>
Date: Mon, 27 Jun 2005 16:38:49 +0100

The Chemistry Development Kit (CDK) can do this, although I am not sure
of the details. You will need to write a program in Java to access the
relevant classes.

http://almost.cubic.uni-koeln.de/cdk/cdk_top

Regards,
Noel

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From: Rajarshi Guha <rxg218<<at>>psu.edu>
Date: Mon, 27 Jun 2005 12:04:57 -0400

> function of exporting 2D structures to picutures. Thanks in advance!

The CDK (  http://almost.cubic.uni-koeln.de/cdk/ ) can do this. There is
an example program at

 http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d

(Currently it only takes SDF as input)

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From: Miklos Vargyas <mvargyas|at|chemaxon.com>
Date: Mon, 27 Jun 2005 18:26:58 +0200

Dear Liu,

MolConverter can do this job for you. It can output both 2D structure 
files and 2D images in various formats. Please follow this link 
http://www.chemaxon.com/marvin/doc/user/molconvert.html for more details.
MolConverter is pure Java so you can run it on all Java enabled 
platforms including Linux too. It's free for academia, you may wish to 
look at  http://www.chemaxon.hu/forum/ftopic193.html.

Hope you'll like it.

Regards,
Miklos Vargyas

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From: Boris Gorelik <bgbg (a) pob.huji.ac.il>
Date: Mon, 27 Jun 2005 21:57:21 +0300

> function of exporting 2D structures to picutures. Thanks in advance!
If you don't need to do this in a script, and if you need to process only a 
few molecules, try this: 
convert the molecule to SMILES (openbabel does this very well), then launch a 
xdrawchem, choose Tools->Input SMILES and paste the SMILES file you've just 
created, then File->Save Picture

XDrawChem has an option of opening SMILES files directly, but on my computer 
this does not work.

Both XDrawChem and opebabel are free (GPL): http://openbabel.sourceforge.net/ 
and  http://xdrawchem.sourceforge.net/

-- 
Boris Gorelik

Mon, 27/Jun/2005, 21 Sivan 5765
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