Egon, I have lost oversight on what the development stands. I need to check with my developers. Mark has left the team, as you might know.
Kind regards,
Chris
--
Dr. Christoph Steinbeck
Head of Cheminformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640
What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..
On 26 Feb 2012, at 09:52, Nina Jeliazkova wrote:
> Hello Egon,
>
> On 26 February 2012 10:31, Egon Willighagen <egon.willighagen@...> wrote:
>> Hej Nina,
>>
>> On Sun, Feb 26, 2012 at 9:17 AM, Nina Jeliazkova
>> <jeliazkova.nina@...> wrote:
>>> I had (may be unrealistic) expectations, that different
>>> implementations of IAtomContainer can always be used together
>>> transparently.
>>
>> The primary idea is the use either one or the other, but combining
>> them should just work. If not, I see that as a grave bug.
>>
>>> However, trying to let JChemPaint working with a molecule, created
>>> by SilentChemObjectBuilder, gives the following error, when trying to
>>> add a new atom via the user interface. The initial molecule is
>>> displayed fine.
>>>
>>> Exception in thread "AWT-EventQueue-0" java.lang.ArrayStoreException:
>>> org.openscience.cdk.silent.Atom
>>> at org.openscience.cdk.Bond.<init>(Bond.java:156)
>>> at org.openscience.cdk.DefaultChemObjectBuilder.newElectronContainerInstance(DefaultChemObjectBuilder.java:373)
>>> at org.openscience.cdk.DefaultChemObjectBuilder.newInstance(DefaultChemObjectBuilder.java:103)
>>> at org.openscience.jchempaint.controller.ControllerHub.addAtomWithoutUndo(ControllerHub.java:613)
>>> at org.openscience.jchempaint.controller.AddBondDragModule.mouseClickedUp(AddBondDragModule.java:224)
>>> at org.openscience.jchempaint.controller.ControllerHub.mouseClickedUp(ControllerHub.java:296)
>>> at org.openscience.jchempaint.controller.SwingMouseEventRelay.mouseReleased(SwingMouseEventRelay.java:107)
>>
>> Yeah, I fixed a number of such issues lately. In fact, I think you are
>> looking for this fix:
>>
>> git show 5bef796b1e12994668dc8a389bde37546ed04ad2
>>
>> And, yes, that was applied *after* 1.4.5...
>>
>>> The JChemPaint 3.3.0 compiled with CDK 1.4.5 is embedded in another
>>> application, the molecule is created by the application, launching
>>> JChemPaint panel is just one of the options to enter a molecule.
>>
>> Rebasing it on top of 1.4.7 should help a lot.
>>
>
> Thanks, this is encouraging :)
>
> Is anybody interested in a patch to the JCP build file to generate a
> jar without CDK and other dependencies (useful for configuring Maven
> project with already defined dependencies) ?
>
> Nina
>
>> Egon
>>
>> --
>> Dr E.L. Willighagen
>> Postdoctoral Researcher
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> 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
>>
>> ------------------------------------------------------------------------------
>> Virtualization & Cloud Management Using Capacity Planning
>> Cloud computing makes use of virtualization - but cloud computing
>> also focuses on allowing computing to be delivered as a service.
>> http://www.accelacomm.com/jaw/sfnl/114/51521223/
>> _______________________________________________
>> Cdk-devel mailing list
>> Cdk-devel@...
>> https://lists.sourceforge.net/lists/listinfo/cdk-devel
>
> ------------------------------------------------------------------------------
> Virtualization & Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> Cdk-devel mailing list
> Cdk-devel@...
> https://lists.sourceforge.net/lists/listinfo/cdk-devel
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