[Joelib-help] Re: JOELib web page 'Applications'

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

Dear Dong Sun Park,

> I'm using your JOELib at my work, It's very useful for me.
Fine.
Please use the mailing lists to avoid me answering questions twice.
http://sourceforge.net/mail/?group_id=39708
Analoge mail (deprecated):
http://sourceforge.net/mailarchive/message.php?msg_id=4505039

> When I convert SMILES to MOL file using Convert script. I got a Mol file without coordinate of atoms.
> all of coordinate are 0. I really need convert program. 
> you have this kind of function in the JOELib, 
> If you don't have it. Would you recommed any program I can use convert function...
To formalize things, i would distinguish between those two functionalities:

1. Conversion: For me this means that atom types are mapped correctly
between formats and that the internal atom typer and the internal expert
systems work correctly. You can also define in this step your own
protonation model, if you want.

2. 2D/3D structure generation: This means that there exists a graph
layout algorithm optimized for the layout of molecular structures.
JOELib provides three possibilities:
2.1. CDK-2D-Layout using joelib.util.cdk.CDKTools
2.2. slow 3D-Layout using MM: joelib.util.ghemical.GhemicalInterface
     This is restricted to Linux systems with IBM-Java-SDK and
     Windows-Cygwin, because it uses a platform dependant JNI-interface
2.3. fast 3D-Layout using Corina (not public, but available): Interface
     works only with a piping mechanism, which is only available for
     Linux systems (Corina problem)

Other possibilities would be:
- CDK: primitive atom typer and expert systems, e.g. good aromaticity
       detection
- Marvin: Good beans interface and commercial

Kind regards, Joerg

-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
                                    (E. Hemingway)

Never mistake action for meaningful action.
                               (Hugo Kubinyi,2004)