Hi Dmitry,
On 28 July 2011 11:28, Dmitry Katsubo <[email protected]> wrote:
> Hi Nina,
>
> Thanks for you reply. Sorry for some delay with the answer...
>
> Thank you for nice demo of rendering the molecule set. From the link to
> maillist I've found the class that does the job:
>
> >
> https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-jchempaint/src/main/java/ambit2/jchempaint/CompoundImageTools.java
There are actually two implementations, if you use cdk 1.3.8 and the cdk
rendering package, instead of JChemPaint, this one is preferred:
https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java
> and also nice work is presented here:
>
> http://gilleain.blogspot.com/2010/09/molecule-layouts.html
> https://sourceforge.net/mailarchive/message.php?msg_id=26495170
>
> Are there any plans to contribute any "layouting" code to jchempaint?
>From my side it is more question of time to contribute the code to the
cdk-render package.
> If
> not, maybe I can re-use the maven module, that contains
> CompoundImageTools / GridMoleculeSetLayout class?
>
>
Yes, here it is for CompoundImageTools :
http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;quick~ambit2-rendering
(depends on cdk-render module)
or
http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;quick~ambit2-jchempaint
(depends on jchempaint)
> I have also run the following related issue. When trying to render the
> molecule like below:
>
> InChI=1/H2/h1H
>
Sounds like the scaling doesn't work when there are no heavy atoms?
http://apps.ideaconsult.net:8080/ambit2/depict?search=%5BH%5D%5BH%5D
InChI=1/H2N/h1H2/q-1
>
>
This renders with non-zero rectangle (cdk 1.3.8)
http://apps.ideaconsult.net:8080/ambit2/depict/cdk?search=InChI%3D1%2FH2N%2Fh1H2%2Fq-1
Best regards,
Nina
chemicalMoleculeRenderer.paint() returns the rectangular with zero
> height and width. Is there any "correct" way to render "simple"
> molecules like that?
>
> The relative message is:
> https://sourceforge.net/mailarchive/message.php?msg_id=27010062
>
> Thanks!
>
> On 02.06.2011 7:22, Nina Jeliazkova wrote:
> > On 2 June 2011 01:38, Dmitry Katsubo <[email protected]> wrote:
> >> I definitely missed that, but perhaps I've joined just shortly
> >> afterwards or it was in jcpempaint maillist (which I need to be
> >> subscribed too):
> >>
> >
> https://sourceforge.net/mailarchive/forum.php?thread_name=4d8097d191b34_300c11a312c6527%40zx81.mail&forum_name=cdk-jchempaint
> >
> http://apps.ideaconsult.net:8080/ambit2/depict?search=CCC.CCC.CCCCCCCC.CCCCCC
> >
> >> Looks great. Is the source open?
> >
> > Yes, it's quite old project ( ambit.sourceforge.net ) and there is a
> recent paper
> > http://www.jcheminf.com/content/3/1/18
> >
> >> Perhaps you can point me directly to the message you refer: if it
> >> contains the implementation hints, I will start from that.
> >
> > Several messages here, where I was struggling with the same problem.
> >
> >
> http://sourceforge.net/mailarchive/forum.php?forum_name=cdk-devel&max_rows=25&style=ultimate&viewmonth=201010&viewday=26
> >
> > Best regards,
> > Nina
>
>
> --
> With best regards,
> Dmitry
>
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