Subject: Re: CCL:SUMARRY --- 3D->2D softwares?

From: "JunJun Liu" <ljjlp03 !! gmail.com>
Date: Sat, 02 Jul 2005 09:53:59 +0800

Deal All:

After receiving Ogham academic licenses now, I can evaluate all the  
recommended programs. Thanks all that gave me advices! I have a lot of  
molecules to be converted to 2D images, so a command line program is more  
of interest. Among the below recommended softwares, I like MolConverter  
and Ogham most, although these two programs still have some shortcomes.
Molconverter:
1. works well only when remove all hydrogens.
2. it has some problem in recognizing some aromatic rings.

Ogham:
1. works a slightly better and smarter, but the program could be used for  
only two months with an academic license.
2. the produced images will be stamped with an OpenEye logo.

----- Recommended Softwares -------
MolConverter (in the package of Marvin)
http://www.chemaxon.hu/marvin/

JChemPaint
http://jchempaint.sf.net/

Ogham
one product of OpenEye Scientific Softwares.
http://www.eyesopen.com/products/toolkits/ogham.html

xdrawchem
http://xdrawchem.sourceforge.net/

CACTVS
http://www.xemistry.com
------------------------------

Best Regards!

Liu

On Mon, 27 Jun 2005 15:56:15 +0800, JunJun Liu <ljjlp03 !! gmail.com> wrote:

> 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

---

From: Ferenc Csizmadia <fcsiz !=! chemaxon.com>
Date: Sat, 02 Jul 2005 22:09:51 +0200

Liu,

Not sure what your specific issues were in the case of MolConverter, but 
I suggest to use our support for help: www.chemaxon.com/forum/
We may be able suggest some settings to improve the quality or to 
customize the image.

Some comments about yours. There is no aromatic ring recognition at all 
if you use the default settings. If you want to see "aromatized" 
structures, you have to use some parameter settings. There are 3 related 
options:
"a": level 1 aromatization
"a_day": level 2 aromatization (more general than level 1)
- "-a"  dearomatization (Kekule representation instead of aromatic)
Example: level 2 aromatization, 600x600 pixels, remove hydrogens
molconvert png:a_dayw600-H input.mol >output.png

I hope this helps.

Best regards,
Ferenc
PS: The next version of JChem (and maybe Marvin) will support 
template-based 2D cleaning, so users will be able to define rules for 
the 2D representation.

JunJun Liu wrote:

> recommended programs. Thanks all that gave me advices! I have a lot 
> of  molecules to be converted to 2D images, so a command line program 
> is more  of interest. Among the below recommended softwares, I like 
> MolConverter  and Ogham most, although these two programs still have 
> some shortcomes.
> Molconverter:
> 1. works a slightly better and smarter, but the program could be used 
> for  only two months with an academic license.
> On Mon, 27 Jun 2005 15:56:15 +0800, JunJun Liu <ljjlp03 !=! gmail.com> wrote:
>
>> Dear All:
>>
>> Is there a software in linux can convert 3D small organic structures 
>> to  2D