On 24 October 2010 23:37, gilleain torrance <gilleain.torrance@...:
> On Sun, Oct 24, 2010 at 8:53 PM, Nina Jeliazkova
> <jeliazkova.nina@...> wrote:
> >>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 ?
> Well, the difficulty comes when the bounding rectangle is calculated
> on atom positions (which are points). For a single atom, this is a
> single point, which is - according to Euclid - "that which has no
> part". In other words, no width or height and a bounds of (x,y,0,0).
> Text, on the other hand, has a definite size.
> > Is it possible to use the same "cleanup" method outside of JCP, for
> > for rendering images like this
> Thanks for the links, it's good to see how JCP rendering compares to
> other toolkits. Badly, it seems...
Well, these two are not good examples I admit ...
> 1) Either the bonds are being drawn on top of the atom symbols, or the
> symbol background is not drawn.
Well, it was working fine in the previous setup (cdk 1.3.3 & JCP 3.0.1) but
today I've upgraded to cdk 1.3.6 and JCP 3.1.3 and something has changed
outside of my code ...
> 2) In the phosphyl-cysteine thing, the atom symbols are not centered
> on the atom positions.
Interestingly, this doesn't have the same issue
> 3) Hydrogens are missing from the NH4+ ion and amine groups - that
> could be due to a preference setting I guess.
It's default preferences - could you give me a hint how to set preferences
in code, without touching JCP properties ?
> 4) The counter-ion text font is very different size to the larger
Yep, this is because of me allocating equal size boxes for the two (or more
if any) parts and scaling each structure separately. Is it possible to
force same scaling ?
> So you could use the ControllerHub without JCP, certainly. It's in the
> controlbasic module, and could be used without connecting up all the
> bits. That is, you wouldn't be interacting with the images that you
> produce by a servlet, but you could pass in null for references to
> things that aren't being used.
> Of course, it would be nicer if there were dedicated MoleculeSetLayout
MoleculeSet is a slightly different thing IMHO, just having a single
procedure to get an image of this kind of disconnected structures would save
lot of time.
Thanks for the quick reply this late!