> > I've worked a bit on Jmol's build.xml... it's not really split up, but if
> > you check out Jmol CVS HEAD, and do 'ant apisio-dist'. It goes on on what
> > you did with the apisio.classes file, which I slightly modified... it now
> > builds a distrib from which I can compile jmolApis.jar and jmolIO.jar...
> > and CDK can be compiled using these...
> >
> > So, I hope this cleans up the circular dependency properly...
>
> Yes, this is a possible solution.
>
> One thing I want to ask: Why these classes don't go into the cdk project
> (into an own module, e.g. cdk-jmol.jar)? 

Convenience for the CDK developers I guess... From CVS, things compile 
nicely...

> Is there any reason, that this circular dependency is still kept?

No special reason...

But is this setup not working for you:

1. build jmol-api deb from jmolApiosIO-bla.tar.gz
2. build CDK deb based on that jmol-api deb
3. build jmol deb from the regular jmol-bla.tar.gz

?

Egon



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