On 25 October 2010 08:09, Nina Jeliazkova <jeliazkova.nina@gmail.com> wrote:


On 25 October 2010 00:10, Egon Willighagen <egon.willighagen@gmail.com> wrote:
On Sun, Oct 24, 2010 at 10:51 PM, Nina Jeliazkova
> On 24 October 2010 23:37, gilleain torrance <gilleain.torrance@gmail.com>
> wrote:
>> > http://apps.ideaconsult.net:8080/ambit2/depict?search=[NH4%2B].CP%28%3DO%29%28O%29CCC%28N%29C%28%3DO%29[O-]
>> 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 ...

I was wondering why the formal charge is not showing up...

It does, but is a bit misplaced.

Here is how it is rendered with the JCP 3.0.1 (cdk 1.3.3 if that matters)

http://pirin.uni-plovdiv.bg:8080/malaria/depict/cdk?search=CP%28%3DO%29%28O%29CC%28c1ccccc1%29C%28N%29C%28%3DO%29[O-].[NH4%2B]&w=600

and  JCP 3.1.3  (cdk 1.3.6 )

http://apps.ideaconsult.net:8080/ambit2/depict/cdk?search=CP%28%3DO%29%28O%29CC%28c1ccccc1%29C%28N%29C%28%3DO%29[O-].[NH4%2B]&w=600


In addition, in both cases, all labels in the right drawing rectangle are misplaced  (could be something related to the nonzero offset of the right drawing rectangle ?  )

http://apps.ideaconsult.net:8080/ambit2/depict/cdk?search=[NH4%2B].CP%28%3DO%29%28O%29CC%28c1ccccc1%29C%28N%29C%28%3DO%29[O-]&w=600

I am looking for hints how to improve the rendering, my knowledge of JCP code is rather superficial.

What I would like to do is :

1)  given 2D rectangle, calculate and setup the transformation for the entire molecule (scale, whatever else matters).

2) draw parts of the molecule in subsequent boxes (inside the rectangle), somehow preventing the renderer to fit /scale each part separately.

Do you think this is possible (and if yes, how) ?

Thanks,
Nina
 

What is the code you are using?


https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-jchempaint/src/main/java/ambit2/jchempaint/CompoundImageTools.java

Nina
Egon

--
Dr E.L. Willighagen
Postdoctoral Research Associate
University of Cambridge
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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