Subject: mol-3D-2D

From: [email-masked]
Date: Thu, 29 Nov 2001 18:00:13 +0100

Hi CCL-ers,
          Does anybody know/currently write/
need  a tool that converts mol-files with 3D - coordinates
into mol-files with 2D - coordinates and correct stereo-
chemisty, up/down bonds etc.. and the same atom numbering
as the original file.
          A tool that could reassign original atom numbering
of the 3D-file a correct 2D-file with changed order of atoms
would do as well.

Greetings,

Maria

---

From: Ferenc Csizmadia <[email-masked]>
Date: Thu, 29 Nov 2001 22:16:50 +0100

Maria,

>of the 3D-file a correct 2D-file with changed order of atoms
There is a command-line tool that can do that in the Marvin Beans 
package of ChemAxon. The tool is called MolConverter. It interconverts 
various file formats (Molfile, SDF, SMILES, ....) and also creates image 
files. I guess you need Molfile to Molfile or SDfile to SDfile 
conversion. (The same atom numbering is applied in the generated 2D-file 
as in the original 3D file)

If you would like to try MolConverter, select "Marvin" at 
http://www.chemaxon.com/products.html and then choose "Download". On the 
download page select "Downloads for web and software developers. 
(Applets and JavaBeans) 
<http://www.chemaxon.com/marvin/devel-download.html> ". (I guess, you 
are not a software developer, but usually developers are interested in 
Marvin Beans)

Since Molconverter is in Java, you need to install a Java Runtime 
Environment before running it. The page explains how to register before 
downloading and how to get Java. When you are done, select the 
marvinbeans-.....zip link. Unzip the file, go to the marvinbeans 
directory (in a Command Prompt or a Unix shell window) and run
    bin_MSWIN\molconvert  mol -2:O1 filename  (in Windows)
    bin/molconvert mol -2:O1 filename  (in Unix)
    (if you need a format other than Molfile, then replace "mol" with 
the abbreviation of another format)
A user guide for Molconverter is available at
    http://www.chemaxon.com/marvin/doc/molconvert.html.

Another product called JChem (it is for chemical database handing) also 
includes the MolConverter. But probably you are better off with Marvin 
Beans, since it is smaller.

Please let me me know if you need help.

Best regards,
Ferenc

-- 
Dr. Ferenc Csizmadia
ChemAxon Ltd.
http://www.chemaxon.com
T:+3620 9570988