Hi Gilleain,



>Hi Nina,

>I'm in the middle of struggling with layouts of molecule sets, so this
>kind of thing is on my mind :)

>JCP doesn't handle layout of disconnected atom containers very well,
>but the ControllerHub method "cleanup" will check for this situation
>and try to place separate parts with non-overlapping bounding boxes.

OK, good to know.



>However, it does occur to me as I say this... single-atom salts (like
>Na+) are just text, and the bounds may not be computed properly,
>sorry. Text is really a pain.

Hm, couldn't it be treated as a single atom, not just text ?


>So cleanup might be worth a try, but I'm not 100% certain it will work.

I've tried cleanup via user interface and it seems to work, except for as you said, single atom salts.

Is it possible to use the same "cleanup" method outside of JCP, for example for rendering images like this

http://apps.ideaconsult.net:8080/ambit2/depict?search=[O-]C1%3DCC%28[N%2B]%28[O-]%29%3DO%29%3DCC%3DC1OC.[Na%2B]

or

http://apps.ideaconsult.net:8080/ambit2/depict?search=[NH4%2B].CP%28%3DO%29%28O%29CCC%28N%29C%28%3DO%29[O-]

(currently it uses somewhat crude hack of my own).

Thanks,
Nina

>gilleain