From: Egon W. <ego...@gm...> - 2012-08-01 12:24:03
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Ralf, On Wed, Aug 1, 2012 at 1:54 PM, Egon Willighagen <ego...@gm...> wrote: > I am going to try again, but will first checkout the source code... Please find attached two first initial patches... (no idea if other will follow... I rather focus on getting the CDK-JChemPaint patch cleaned up further)... But, one patch removes a class which is completely unrelated to rendering/controlling and explains the dependency on the qm module. The other patch is one you should have a close look at... the instanceof should be done against the interface, not an particular interface implementation (so, IBond instead of Bond)... now, for data/nonotify that went well, because "Bond" was the 'data' implementation and the NNBond implementation from the 'nonotify' module, this may have worked... however, the silent 'IBond' implementation does *not* extend the 'data' implementation... I fixed two classes, but if you run into more such code... 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: Ralf S. <ra...@ar...> - 2012-08-01 14:23:28
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Thanks for the patches, Egon. I've looked them through and they apply cleanly. If they fix some behaviour (with reactions possibly, I haven't had a look at that part of JCP but there are many issues with it), can you suggest a test for it? |
From: Egon W. <ego...@gm...> - 2012-08-01 14:26:45
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On Wed, Aug 1, 2012 at 4:17 PM, Ralf Stephan <ra...@ar...> wrote: > Thanks for the patches, Egon. > I've looked them through and they apply cleanly. > If they fix some behaviour (with reactions possibly, I haven't > had a look at that part of JCP but there are many issues with it), > can you suggest a test for it? Not in terms of the unit test framework... But some were found by adding a molecule as reactant and as product to a reaction. I have another problem, which I have not fixed yet, occurs when you created a simple reaction, then edit a structure, and try to save as MDL RXN... it will then complain about molecules not in a IReaction... (it should be empty, but should empty IAtomContainers should not be written anyway...) 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: Ralf S. <ra...@ar...> - 2012-08-01 14:48:05
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On Wed, Aug 01, 2012 at 04:26:18PM +0200, Egon Willighagen wrote: > But some were found by adding a molecule as reactant and as product to > a reaction. Consider me completely naive on reactions. How is the above supposed to be done? |
From: Egon W. <ego...@gm...> - 2012-08-01 14:55:37
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On Wed, Aug 1, 2012 at 4:42 PM, Ralf Stephan <ra...@ar...> wrote: > On Wed, Aug 01, 2012 at 04:26:18PM +0200, Egon Willighagen wrote: >> But some were found by adding a molecule as reactant and as product to >> a reaction. > > Consider me completely naive on reactions. How is the above > supposed to be done? Yeah, sorry... right click on an atom -> Reaction -> Add to new reaction ... (or one of the other three options) 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: Ralf S. <ra...@ar...> - 2012-08-01 16:56:24
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On Wed, Aug 01, 2012 at 04:26:18PM +0200, Egon Willighagen wrote: > But some were found by adding a molecule as reactant and as product to > a reaction. > > I have another problem, which I have not fixed yet, occurs when you > created a simple reaction, then edit a structure, and try to save as > MDL RXN... it will then complain about molecules not in a IReaction... > (it should be empty, but should empty IAtomContainers should not be > written anyway...) The cdkapi-1.5 branch of rwst/jchempaint is supposed to be compatible with CDK master. Included is a commit that changes all occurences of IMolecule(Set) to IAtomContainer(Set), at least I thought so. Now I see that the usage of cdk-silent.jar on one hand and the patches you just sent presuppose that this commit was applied to the JCP branch compatible with CDK-1.4.x, not 1.5. So I applied the commit which, if this all is right, I should have applied immediately. It also transpires that the commit does not suffice and there are still changes to be made. This means, Egon, please just wait a bit with further patches until I'm done and that specific ripple is through the codebase. Quite possibly some of your problems might magically go away. |
From: Egon W. <ego...@gm...> - 2012-08-01 18:04:57
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On Wed, Aug 1, 2012 at 6:50 PM, Ralf Stephan <ra...@ar...> wrote: > This means, Egon, please just wait a bit with further patches until I'm > done and that specific ripple is through the codebase. Quite possibly some > of your problems might magically go away. OK :) I had an itch... I'm trying to get me Groovy Cheminformatics book done, and was working on the reactions chapter... so, I needed the rendering :) See: https://plus.google.com/u/0/104186710895049917005/posts/Pv2CNcNyM7K 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: Ralf S. <ra...@ar...> - 2012-08-01 17:27:25
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Actually, the commit IS only compatible with CDK-1.5 because for example the cdk-1.4.x branch of cdk/cdk still has a method interfaces.IChemModel:setMoleculeSet that expects an IMoleculeSet! So, I won't apply it and will move usage of cdk-silent into JCP's cdkapi-1.5 branch. Please, also check that any future patches to JCP have some info to which of the 1.4/1.5 it applies. On Wed, Aug 01, 2012 at 06:50:46PM +0200, Ralf Stephan wrote: > On Wed, Aug 01, 2012 at 04:26:18PM +0200, Egon Willighagen wrote: > > But some were found by adding a molecule as reactant and as product to > > a reaction. > > > > I have another problem, which I have not fixed yet, occurs when you > > created a simple reaction, then edit a structure, and try to save as > > MDL RXN... it will then complain about molecules not in a IReaction... > > (it should be empty, but should empty IAtomContainers should not be > > written anyway...) > > The cdkapi-1.5 branch of rwst/jchempaint is supposed to be compatible > with CDK master. Included is a commit that changes all occurences of > IMolecule(Set) to IAtomContainer(Set), at least I thought so. > > Now I see that the usage of cdk-silent.jar on one hand and the patches > you just sent presuppose that this commit was applied to the JCP branch > compatible with CDK-1.4.x, not 1.5. So I applied the commit which, if > this all is right, I should have applied immediately. It also transpires > that the commit does not suffice and there are still changes to be made. > > This means, Egon, please just wait a bit with further patches until I'm > done and that specific ripple is through the codebase. Quite possibly some > of your problems might magically go away. > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint |
From: Egon W. <ego...@gm...> - 2012-08-01 18:06:13
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On Wed, Aug 1, 2012 at 7:21 PM, Ralf Stephan <ra...@ar...> wrote: > Please, also check that any future patches to JCP have some info to which of the 1.4/1.5 it applies. Yeah, sorry about that. I worked against master, and did not think of it... Which of the two do you prefer me to work on? 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: Ralf S. <ra...@ar...> - 2012-08-01 18:30:01
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On Wed, Aug 01, 2012 at 08:05:44PM +0200, Egon Willighagen wrote: > On Wed, Aug 1, 2012 at 7:21 PM, Ralf Stephan <ra...@ar...> wrote: > > Please, also check that any future patches to JCP have some info to which of the 1.4/1.5 it applies. > > Yeah, sorry about that. I worked against master, and did not think of it... > > Which of the two do you prefer me to work on? 1.4 if you don't mind, thanks. |
From: Ralf S. <ra...@ar...> - 2012-08-03 07:17:35
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On Wed, Aug 01, 2012 at 04:26:18PM +0200, Egon Willighagen wrote: > I have another problem, which I have not fixed yet, occurs when you > created a simple reaction, then edit a structure, and try to save as > MDL RXN... it will then complain about molecules not in a IReaction... > (it should be empty, but should empty IAtomContainers should not be > written anyway...) If you're not working on this, can you please put it in the tracker? |
From: Egon W. <ego...@gm...> - 2012-08-03 12:49:00
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On Fri, Aug 3, 2012 at 9:11 AM, Ralf Stephan <ra...@ar...> wrote: > If you're not working on this, can you please put it in > the tracker? https://github.com/JChemPaint/jchempaint/issues/110 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 |