[Joelib-help] Atom symbols in JOELib visualization ?

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

Dear Dr. Karthikeyan,

> Is there any provision to see atom symbols in molecule viewer especially
I assume that you are using the 3D viewer.

1. You can see atom symbols in the 2D viewer (not directly accessible 
from a testing method), but you can e.g. simply use the PDF output, 
which uses the 2D viewer funcionality:
sh convert.sh test.sdf test.pdf

There is a huge amount of properties for this visualization in the 
joelib.properties-file available:
joelib.gui.render.Renderer2DModel.*
joelib.gui.render.Mol2Image.*
joelib.io.types.PDF.*

The most relevant will be:
joelib.gui.render.Renderer2DModel.drawNumbers=false
joelib.gui.render.Renderer2DModel.useKekuleStructure=false
joelib.gui.render.Renderer2DModel.showEndCarbons=true
joelib.gui.render.Renderer2DModel.atomColoring=false

joelib.gui.render.Mol2Image.defaultWidth=500
joelib.gui.render.Mol2Image.defaultHeight=400

!!! First additional remark !!! The PDF output MUST store all molecules 
in the memory, so it can be used only for a small number of molecules, 
especially if they have a huge amount of descriptors, because they are 
printed to PDF also.
!!! Second additional remark !!! There is no 2D layout algorithm 
directly available but the CDK interface supports such things, but this 
is not available directly, because this is an optional functionality.

2. In the Java3D viewer are until now no atom symbols available.

Kind regards, Joerg

> 
> in the 'wire' mode?
> 
> regards
> 
> --
> M. Karthikeyan, Ph.D., Scientist
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-- 
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
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