Re: [Joelib-help] draw molecule

[Joerg K. W. <we...@in...>]

Hi Andreas,

two problems occur:
1. log4j.properties is missing in the classpath or starting directory
2. You do not have ANY 2D coordinates. Creating them is not an easy task 
and you can e.g. use CDK under JOELib with:
joelib.util.cdk.CDKTools
joelib.util.cdk.TestLayout
but you will need all CDK libraries under joelib/lib

You can eventually (IBM-JRE-Linux only or Windows/Cygwin from command 
line) Ghemical for 3D coordinates, but that might be tricky, because it 
uses JNI:
joelib.util.ghemical.TestInterface

Or implement you own 2D layout (with constraints) as proposed by Rarey 
et al.:
http://dx.doi.org/10.1021/ci049958u

Kind regards, Joerg

>>please try
>>joelib.gui.render.MoleculeViewer2D
>>
>>Have a look at the main method and for details:
>>display(JOEMol molecule, String _title,
>>        JOESmartsPattern smarts, String eTransfer, String retroSynth,
>>        String conjRing, String labels)
>>
> 
> 
> Hi Joerg,
> 
> I tried like this:
> 
> import joelib.molecule.*;
> import joelib.smiles.*;
> import joelib.gui.render.*;
> 
> 
> public class SmilesSmartsViewer {
> 
> 	public static void main(String[] args) {
> 		 
> 		 // obtain smiles string and create mol object
> 		 String smiles="C1CCCCC1";	// the smiles string
> 		JOEMol mol=new JOEMol();	// create new mol-object
> 		 
> 		 // convert mol object to represent the smiles information
> 		 if (!JOESmilesParser.smiToMol(mol, smiles, smiles))
> 		 {
> 		   System.err.println("SMILES entry \"" + smiles + "\" could not be loaded.");
> 		 }
> 		
> 		// display mol object
> 		MoleculeViewer2D.display(mol);
> 	}
> }
> 
> 
> Output is as follows here:
> 
> log4j:WARN No appenders could be found for logger (joelib.io.IOType).
> log4j:WARN Please initialize the log4j system properly.
>  t1 t2 t3 t4 t5 t6
>  t1 t2 t3 t4 t5 t6
>  t1 t2 t3 t4 t5 t6
>  t1 t2 t3 t4 t5 t6
>  t1 t2 t3 t4 t5 t6
>  t1 t2 t3 t4 t5 t6
>  t1 t2 t3 t4 t5 t6
> frag 0 has 6 atoms
>  t1 t2 t3 t4 t5 t6
> 
> A window opens but remains blank!
> What's the error?
> 
> Kind regards,
> 
> Andreas
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: Oracle 10g
> Get certified on the hottest thing ever to hit the market... Oracle 10g. 
> Take an Oracle 10g class now, and we'll give you the exam FREE.
> http://ads.osdn.com/?ad_id=3149&alloc_id=8166&op=click
> _______________________________________________
> Joelib-help mailing list
> Joe...@li...
> https://lists.sourceforge.net/lists/listinfo/joelib-help
> 


-- 
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)