From: Nina J. <jel...@gm...> - 2012-02-26 08:17:33
|
Hi All, Yet another finding this week. I had (may be unrealistic) expectations, that different implementations of IAtomContainer can always be used together transparently. 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) 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. Am I missing something? Should a molecule from cdk-silent accept atoms from e.g. cdk-data package and vice versa? Best regards, Nina |
From: Egon W. <ego...@gm...> - 2012-02-26 08:31:28
|
Hej Nina, On Sun, Feb 26, 2012 at 9:17 AM, Nina Jeliazkova <jel...@gm...> 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. 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 |
From: Nina J. <jel...@gm...> - 2012-02-26 08:53:03
|
Hello Egon, On 26 February 2012 10:31, Egon Willighagen <ego...@gm...> wrote: > Hej Nina, > > On Sun, Feb 26, 2012 at 9:17 AM, Nina Jeliazkova > <jel...@gm...> 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...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Christoph S. <ste...@eb...> - 2012-02-26 16:42:20
|
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 <ego...@gm...> wrote: >> Hej Nina, >> >> On Sun, Feb 26, 2012 at 9:17 AM, Nina Jeliazkova >> <jel...@gm...> 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...@li... >> 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...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Egon W. <ego...@gm...> - 2012-02-26 17:18:32
|
On Sun, Feb 26, 2012 at 5:42 PM, Christoph Steinbeck <ste...@eb...> wrote: > 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. Yes, I know. There is no rush. Vedrin and Nina have looked at the remaining patches in the JChemPaint code that need applying to CDK, and that seems minimal, so I will look at that really soon. Shall I check if Nina has commit rights, and just push the addition after I had a look at it? 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 |