Dear Dmitry,
>From the attached picture, it looks like there is another atom being
overlapped behind the Nitrogen being shown, probably another nitrogen.
Is the 'molecule' you're drawing by any chance N2? How did you obtain the
molecule, load it from a mol-file?
The CDK expects bond lengths in files it loads to be around 1.5
(dimension-less, but you can think "angstrom" if that helps you), sometimes
other programs use other scales, and it messes up the drawing.
Regardless, it seems the either the coordinates or the image zoom are not
properly set, so that the atoms symbols are drawn so large that they
overshadow the bonds (which are probably very short from the look of the
picture).
You can use the StructureDiagramGenerator class included in the CDK to
re-layout the molecule; this should solve any problem about the bond-lengths
being weird.
Also it should be noted that the cdk-jchempaint patch is currently under
very heavy development by Egon, and not very stable, I hope you are aware of
that.
Best regards,
Jules Kerssemakers
2011/1/14 Dmitry Katsubo <dmitry.kats...@gmail.com>
> Dear CDK users,
>
> I am using cdk-1.3.8.jar + cdk-jchempaint-16.jar. When I render a
> molecule, only one atom is rendered (see attachment). Can anybody
> provide hint about what combination of CDK and cdk-jchempaint is stable
> or maybe my code is not adequate?
>
> Thanks in advance.
>
> --
> With best regards,
> Dmitry
>
>
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