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From: gilleain t. <gil...@gm...> - 2017-05-22 12:21:37
|
Ok, forgot to mention the standalone app use-case. Sure - that won't go away. Indeed, much of the drawing code is in the core CDK anyway, to allow Bioclipse to use it. On top of that is 'just' a swing app with some buttons, I suppose. I know there's more to it - but don't worry, that should remain as-is, for sure. The only use-case that wouldn't be handled would be a web page with just a sketcher, with no back-end. That would be a shame - especially considering the 2D-to-3D examples that Jmol/JSmol has been experimenting with. At the moment, I'm just trying out various technologies to see which is nicest to use. I'll let people know when there is something too look at. thanks, Gilleain On Mon, May 22, 2017 at 1:07 PM, Nina Jeliazkova <jel...@gm...> wrote: > > > On 22 May 2017 at 15:00, John Mayfield <joh...@gm...> > wrote: > >> For a web front end - there are other JS chemical editors out there >>> indeed. >> >> >> Ah... but a lot of them are pretty rubbish :-). >> > > Very much agree ;) [1] > > My point is different - JCP as a java dependency for standalone > application is a valid use case - and it is better to be kept as such, > without introducing web service dependency. > > (also agree that single object model is not necessary the right choice for > all use cases) > > > Regards, > Nina > > > [1] https://twitter.com/10705013/status/448160308042162177 > > >> We were trying to find once recently at NextMove to handle reactions and >> basically with the exception of MarvinJS they were all terrible move agents >> to reactants etc add superfluous grouping. >> >> John >> >> On 22 May 2017 at 12:55, John Mayfield <joh...@gm...> >> wrote: >> >>> 2) Port (cross-compile? transpile?) JCP to Javascript >>> >>> >>> This would be my preference, but my understanding is with GWT etc would >>> essentially be a re-write. IIRC MarvinJS (https://www.chemaxon.com/prod >>> ucts/marvin/marvin-js/) is done using GWT but you'll notice it's very >>> different from their MarvinSketch applet. >>> >>> I think it's best to do a lighter weight model for the sketcher with the >>> "chemical intelligence" handled by WS as you suggest. I actually don't >>> think a sketcher should use the same object model (OM) at all. There are >>> lots of things useful to capture in a sketch which just doesn't make sense >>> to represent in data. >>> >>> After working with it a fair bit I feel ChemDraw have basically nailed >>> the OM required for sketching, it's not perfect but very close and captures >>> many intricacies. >>> >>> e.g. Character attach information allows you do the following: >>> >>> OH >>>> | >>>> -C(CH2CHO)- >>> >>> >>> e.g. Which side of a bond the double bond line goes: >>> http://www.cambridgesoft.com/services/documentation/sdk/chem >>> draw/cdx/properties/Bond_DoublePosition.htm >>> >>> John >>> >>> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint > > |
From: Nina J. <jel...@gm...> - 2017-05-22 12:07:43
|
On 22 May 2017 at 15:00, John Mayfield <joh...@gm...> wrote: > For a web front end - there are other JS chemical editors out there >> indeed. > > > Ah... but a lot of them are pretty rubbish :-). > Very much agree ;) [1] My point is different - JCP as a java dependency for standalone application is a valid use case - and it is better to be kept as such, without introducing web service dependency. (also agree that single object model is not necessary the right choice for all use cases) Regards, Nina [1] https://twitter.com/10705013/status/448160308042162177 > We were trying to find once recently at NextMove to handle reactions and > basically with the exception of MarvinJS they were all terrible move agents > to reactants etc add superfluous grouping. > > John > > On 22 May 2017 at 12:55, John Mayfield <joh...@gm...> > wrote: > >> 2) Port (cross-compile? transpile?) JCP to Javascript >> >> >> This would be my preference, but my understanding is with GWT etc would >> essentially be a re-write. IIRC MarvinJS (https://www.chemaxon.com/prod >> ucts/marvin/marvin-js/) is done using GWT but you'll notice it's very >> different from their MarvinSketch applet. >> >> I think it's best to do a lighter weight model for the sketcher with the >> "chemical intelligence" handled by WS as you suggest. I actually don't >> think a sketcher should use the same object model (OM) at all. There are >> lots of things useful to capture in a sketch which just doesn't make sense >> to represent in data. >> >> After working with it a fair bit I feel ChemDraw have basically nailed >> the OM required for sketching, it's not perfect but very close and captures >> many intricacies. >> >> e.g. Character attach information allows you do the following: >> >> OH >>> | >>> -C(CH2CHO)- >> >> >> e.g. Which side of a bond the double bond line goes: >> http://www.cambridgesoft.com/services/documentation/sdk/chem >> draw/cdx/properties/Bond_DoublePosition.htm >> >> John >> >> > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > |
From: Nina J. <jel...@gm...> - 2017-05-22 11:53:11
|
On 22 May 2017 at 14:45, Konstantin Tokarev <an...@ya...> wrote: > > > 22.05.2017, 14:43, "gilleain torrance" <gil...@gm...>: > > Hi, > > Apologies for the cross-post, but I'm not sure how many people are on the > JCP-devel list. > > Anyway, it's clear that Java Applet's days are numbered. > > > Note that it's not only applet, but also stand alone swing application. I > also was using it as a part of OpenOffice.org plugin where Java was obvious > choice. > ... JCP is also used as Java library in several standalone applications . >From our side, it is quite a critical component in standalone Toxtree. For a web front end - there are other JS chemical editors out there indeed. Best regards, Nina > > > > There are a number of options here: > > 1) Abandon JCP - there are other JS chemical editors out there! > 2) Port (cross-compile? transpile?) JCP to Javascript > 3) Re-write in JS > > I'm not a fan of option 1) naturally. So I'm wondering if anyone has any > advice on 2) or 3). I note this SO question from Rich Apodaca: > > http://stackoverflow.com/questions/440302/how-to-cross- > compile-java-source-code-to-javascript > > which has led me to various options: > > - GWT (google's toolkit) > - Kotlin (JVM language) > - JSweet (uses Typescript) > - Java2Javascript (used by Jmol) > > However, I'm sure there are others. I will try and experiment with some of > these - starting with JSweet - and will put the results on github. What I'm > likely to try is just some simple vector editing written in Java and > cross-compiled to JS. > > One initial problem is that to get everything into the browser, you have > to cross-compile all the code (including CDK code) and all dependencies to > JS. Not sure how possible that could be. An alternative might be to have a > thin JS client with the view model and a servlet maintaining the domain > model. > > Let me know if you have other ideas, or forsee any problems.. > > Gilleain > , > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > , > > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint > > > > -- > Regards, > Konstantin > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint > > |
From: Konstantin T. <an...@ya...> - 2017-05-22 11:46:00
|
<div> </div><div> </div><div>22.05.2017, 14:43, "gilleain torrance" <gil...@gm...>:</div><blockquote type="cite"><div>Hi,<div> </div><div>Apologies for the cross-post, but I'm not sure how many people are on the JCP-devel list.</div><div> </div><div>Anyway, it's clear that Java Applet's days are numbered.</div></div></blockquote><div><br />Note that it's not only applet, but also stand alone swing application. I also was using it as a part of OpenOffice.org plugin where Java was obvious choice.</div><div> </div><div> </div><blockquote type="cite"><div><div>There are a number of options here:</div><div> </div><div>1) Abandon JCP - there are other JS chemical editors out there!</div><div>2) Port (cross-compile? transpile?) JCP to Javascript</div><div>3) Re-write in JS</div><div> </div><div>I'm not a fan of option 1) naturally. So I'm wondering if anyone has any advice on 2) or 3). I note this SO question from Rich Apodaca:</div><div> </div><div><a href="http://stackoverflow.com/questions/440302/how-to-cross-compile-java-source-code-to-javascript">http://stackoverflow.com/questions/440302/how-to-cross-compile-java-source-code-to-javascript</a></div><div> </div><div>which has led me to various options:</div><div> </div><div>- GWT (google's toolkit)</div><div>- Kotlin (JVM language)</div><div>- JSweet (uses Typescript)</div><div>- Java2Javascript (used by Jmol)</div><div> </div><div>However, I'm sure there are others. I will try and experiment with some of these - starting with JSweet - and will put the results on github. What I'm likely to try is just some simple vector editing written in Java and cross-compiled to JS.</div><div> </div><div>One initial problem is that to get everything into the browser, you have to cross-compile all the code (including CDK code) and all dependencies to JS. Not sure how possible that could be. An alternative might be to have a thin JS client with the view model and a servlet maintaining the domain model.</div><div> </div><div>Let me know if you have other ideas, or forsee any problems..</div><div> </div><div>Gilleain</div></div>,<p>------------------------------------------------------------------------------<br />Check out the vibrant tech community on one of the world's most<br />engaging tech sites, Slashdot.org! <a href="http://sdm.link/slashdot">http://sdm.link/slashdot</a></p>,<p>_______________________________________________<br />Cdk-jchempaint mailing list<br /><a href="mailto:Cdk...@li...">Cdk...@li...</a><br /><a href="https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint">https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint</a></p></blockquote><div> </div><div> </div><div>-- <br />Regards,</div><div>Konstantin</div><div> </div> |
From: gilleain t. <gil...@gm...> - 2017-05-22 11:43:18
|
Hi, Apologies for the cross-post, but I'm not sure how many people are on the JCP-devel list. Anyway, it's clear that Java Applet's days are numbered. There are a number of options here: 1) Abandon JCP - there are other JS chemical editors out there! 2) Port (cross-compile? transpile?) JCP to Javascript 3) Re-write in JS I'm not a fan of option 1) naturally. So I'm wondering if anyone has any advice on 2) or 3). I note this SO question from Rich Apodaca: http://stackoverflow.com/questions/440302/how-to-cross-compile-java-source-code-to-javascript which has led me to various options: - GWT (google's toolkit) - Kotlin (JVM language) - JSweet (uses Typescript) - Java2Javascript (used by Jmol) However, I'm sure there are others. I will try and experiment with some of these - starting with JSweet - and will put the results on github. What I'm likely to try is just some simple vector editing written in Java and cross-compiled to JS. One initial problem is that to get everything into the browser, you have to cross-compile all the code (including CDK code) and all dependencies to JS. Not sure how possible that could be. An alternative might be to have a thin JS client with the view model and a servlet maintaining the domain model. Let me know if you have other ideas, or forsee any problems.. Gilleain |
From: Egon W. <ego...@gm...> - 2014-01-09 14:51:46
|
On Thu, Jan 9, 2014 at 3:29 PM, John May <jo...@eb...> wrote: > As you say a toolkit independent abstraction - however if I were to plug in the > CDK-JChemPaint IUndoRedoable edits into JChemPaint they would not work. Yeah, it does depend on bridges to the various toolkits. Arvid has been doing this for SWT. I do not know what Stefan and Gilleain did for Swing in the JChemPaint applet... I have no insight in what they did in that respect after the fork. > Part of the problem I see is that the granularity ‘ChangeCoordsEdit.java’ > etc isn’t needed - for AtomContainers a more robust approach is to simply > clone the container an push it onto the Undo/Redo stack. That was the original JChemPaint implementation, but was too slow. I would need to dig up more history to see if that was the only reason or not... I do not remember at this moment. Arvid, do you happen to remember the full argumentation for the edit design? > With fewer edit classes it’s now trivial to write the undo/redo manager interaction. That I agree with. > What I really worry about is - > https://github.com/egonw/cdk/tree/13-unsorted-patches/src/main/org/openscience/cdk/controller > and > https://github.com/egonw/cdk/tree/13-unsorted-patches/src/main/org/openscience/cdk/controller/undoredo > > That’s a load much more code to add to an already strained code base. Worst > of all - everything public! and adds to the JavaDoc. I’m really trying to > trim down the bloat and make things more streamlined, efficient and easier > to use. Got it. Maybe with the current CDK just a stack of IChemModel's is now fast enough and the way to go... 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 ORCID: 0000-0001-7542-0286 |
From: Egon W. <ego...@gm...> - 2014-01-09 13:59:38
|
On Thu, Jan 9, 2014 at 2:55 PM, John May <jo...@eb...> wrote: > No, were not using the CDK-JChemPaint as it does not have the editor (i.e. > JChemPaintPanel). Such panels are toolkit (SWT, Swing, ...) specific... that's why. > The JChemPaint-HotFix is based on > https://github.com/jchempaint/jchempaint patched up to 1.5.4. The 1.5.x. > gives us stereochemistry depiction and export to/from SMILES/InChI and > Molfile. I've also stripped out the ability to run as an applet (replaced > the nestedvm inchi with the CDK InChIGenerator) and have added OPSIN for > name-to-structure. There’s still lots more to fix. I don’t have the time to > maintain this to an official capacity but if people want a good working > desktop version of JChemPaint - it’s there. How much copied code is there still in JChemPaint-HotFix? That is, how much of the fork is still left? > Does the CDK-JChemPaint contain those IUndoRedoable? If so I’m sure if this > should be in the main code base. The idea is to have a toolkit-independent abstraction... I think we have that... I can check if you like... > It’s not a very good API and I think it’s > much easier just to write a custom undoable/edit using the Swing or SWT API. I am very happy with the code that Arvid worked on... > Trying to use it in JChemPaint is a pain as the interfaces are merely an > illusion and in reality it just cast to UndoableEdit (Swing API). Are you sure SWT doesn't have a separate API? 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 ORCID: 0000-0001-7542-0286 |
From: Egon W. <ego...@gm...> - 2014-01-09 10:33:47
|
Arvid, John, can you please communicate your works in the area of JChemPaint, CDK-JChemPaint, CDK, etc, etc... Arvid, John has a highlighter patch: https://sourceforge.net/p/cdk/patches/716/ Some output of that is, I guess, visible in the updated screenshots of KNIME-CDK? -> http://metabolights.blogspot.nl/2014/01/knime-cdk-150-released.html John, Arvid has a glow patch: https://github.com/bioclipse/bioclipse.ds/commit/672877ed4ad7b542315968123e361c857f8d9799 John, can you also explain on which "fork" you have been working? The JChemPaint tree, or 'my' CDK-JChemPaint patch? Arvid is working from the CDK-JChemPaint patch, and uses SWT instead of Swing, which is needed for Bioclipse. 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 ORCID: 0000-0001-7542-0286 |
From: Nina J. <jel...@gm...> - 2013-05-27 11:35:43
|
<html> <head> <title>Test PNG transparency</title> </head> <body bgcolor='#f0f0f0'> <img src="test.png" border='1'/> </body> </html> |
From: Egon W. <ego...@gm...> - 2013-05-27 04:48:10
|
Hi all, I am in the preparation of releasing CDK-JChemPaint patch 38, which is rebased on CDK 1.4.8... for all the new people, "CDK-JChemPaint" is the renderer/controler stack patches and not the JChemPaint applet. CDK-JChemPaint is being back-integrated into the CDK, but not all modules are ready yet. The current status of missing unit tests, JavaDoc, etc can be found here: http://pele.farmbio.uu.se/nightly-jcp/ Also note that it has a rendersvg module for which there still is a separate patch in the CDK tracker too. Help with further cleaning up this code is most welcome. I will see what patches from the Bioclipse tree I can pull in as soon as possible... but here too, rebasing patches on the latest CDK-JChemPaint patches are welcome too. Please also note that I have not been able to find time either to look at the JChemPaint release branch. As you know, these branches have severely branched, and identification of features that could be ported to CDK-JChemPaint is still an open task. Ralf has done excellent work in this area already, for which I am very grateful! Next up for me is putting release 38 on SourceForge, updating my "Groovy JChemPaint" code examples [0], create same examples with the controller functionality, and porting the patches to master. There are other things to do, like updating applications/plugins that use JChemPaint, work on the template stack, etc, etc At a design level, these things are still open, and your ideas/work on that is also welcome: 1. fixing the margin/zoom/scale stack The practical issue of getting font sizes right caused this part to be partially implemented. The idea was to fully split world and screen coordinates. Normally the zoom is 1.0, causing the full structure to take up the full image size, expect for the set margins, where the scale exactly matches the coordinate size different. So, if the world size (1D) was 10 angstrom, and the image size 1000, then the scale would be 100. The zoom can then, afterwards, be used to zoom in and out, but when set to 1.0 again, the structure would once again fill the image. 2. two pass drawing Drawing bonds requires knowledge about the drawn atom labels: we do not want to bonds to be drawn where the labels are. This requires a two-pass system, to solve circular dependencies. Here too, btw, the font and thus real-world label size is one troubling part. Egon 0.https://github.com/egonw/groovy-jcp -- 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: Hendrik G. <h.g...@we...> - 2013-05-15 17:35:47
|
Hello, im developing a substructure filter with the CDK. I would like to give user the chance to load molecules from SD files or draw molecules with JChemPaint. How can i integrate JChemPaint in a JPanel or a JFrame? Can you give me an example? Thank you very much! Best regards, Hendrik Göddeke |
From: Egon W. <ego...@gm...> - 2012-12-15 12:15:34
|
Hi Ralf, others, what options exist in JChemPaint regarding interaction from JavaScript? In particular, are there call-back hooks in JS that get called when the user clicks an atom or bond in the applet? 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: <ra...@ar...> - 2012-10-17 07:42:54
|
The new release fixes several bugs. Its testing code is now also deemed robust enough to be fit for automated testing, which needs a virtual X session if you want to implement it. Results from this release are 1 failure in 86 tests (a problem with reaction drawing). What was fixed, apart from test code: #76R undo with chain testcase regression #116 replace atom+undo: exception #129 input via SMILES disturbs later implicit hydrogen calculations #137 merge garbles implicit Hs #139 cut any molecule throws #143R drag bond throws regression #153 merging ethane internally does not delete bond from model #154 merging with chain garbles implicit Hs #156 any non-merging chain + undo --> NPE #158 with chain, single click on atom creates undo slot, should do nothing Regards, Ralf Stephan |
From: <ra...@ar...> - 2012-10-02 17:56:51
|
Hello, Since there is some demand for a finer grained release cycle, and a full maven automation is not in sight (brittle GUI testing being a blocker still), I'm making manual snapshots of my bugfixes branch available at: https://github.com/rwst/jchempaint/downloads The bugfixes branch of rwst/jchempaint is exactly what is merged at the end of the month into JChemPaint/jchempaint:master and released (with a four digit date). The snapshots have a six-digit date so you can see at once which is a monthly and not. This is as nightly as can be, I'm still the only dev and not every day a commit is uploaded. But still, compared with v. 1209, the v. 121002 has two important bugs fixed, so you get real value with every new version. Have fun, Ralf Stephan |
From: Nina J. <jel...@gm...> - 2012-09-29 09:49:57
|
On 29 September 2012 12:56, Angel Herráez <ang...@ua...> wrote: > > H3C---CH3 > > > > Now you drag the bond (only) away, what do you expect happens? > > Ethane moves in full > > Maybe > > > > the bond moves and stays without atoms, > > This makes no sense to me. What is a bond without atoms? > > Exactly. Thus another option - do nothing . > > or the bond disappears, leaving two methanes? > > If I want to separate the two atoms (methanes here), I would try to delete > the > bond, not move it. > > So I vote for option #1. Moving the bond should, if anything, move the > atoms > attached to it. > In case of a fused rings structure this might lead to movement of the entire molecule. Regards, Nina > What happens to other atoms attached to those (i.e. in molecules larger > than > ethane)? They should stay I think, though then you have some very long > bonds. > > > > ------------------------------------------------------------------------------ > How fast is your code? > 3 out of 4 devs don\\\'t know how their code performs in production. > Find out how slow your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219672;13503038;z? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint > |
From: A. H. <ang...@ua...> - 2012-09-29 09:44:05
|
> H3C---CH3 > > Now you drag the bond (only) away, what do you expect happens? > Ethane moves in full Maybe > the bond moves and stays without atoms, This makes no sense to me. What is a bond without atoms? > or the bond disappears, leaving two methanes? If I want to separate the two atoms (methanes here), I would try to delete the bond, not move it. So I vote for option #1. Moving the bond should, if anything, move the atoms attached to it. What happens to other atoms attached to those (i.e. in molecules larger than ethane)? They should stay I think, though then you have some very long bonds. |
From: <ra...@ar...> - 2012-09-29 09:28:46
|
Many thanks. I have an additional question: H3C---CH3 Now you drag the bond (only) away, what do you expect happens? Ethane moves in full, the bond moves and stays without atoms, or the bond disappears, leaving two methanes? Regards, R. Stephan |
From: Nick E. <nic...@gm...> - 2012-09-28 15:05:05
|
Hello Ralf, I would expect for the case of deleting the bond that you would get 2 CH4 molecules. Following on from this, I would expect deleting the bond and C* to give a single CH4. Since users might accidentally add a bond, deleting a bond should be the inverse operation of adding a bond. For me behaving otherwise would be confusing. Nick On 28 September 2012 15:42, Ralf Stephan <ra...@ar...> wrote: > Hello, > I'm looking for feedback on a use case where I'm not sure > what users would expect. As that case results at the moment > in an exception I offer you the choice to decide how I'll fix it. > > H3C---CH3 > > Assume you have ethane on the canvas. Now you click Select > Rectangle and draw a selection rectangle around the first C, > the bond middle not included, so your selection *is practically > the first C. Deletion will leave CH4, and I hope you agree. > > Now draw the rectangle a bit wider such that the bond middle > is included, selecting C *and bond. 1. What will remain when you > delete both? CH4 or nothing? 2. Would you expect deleting the bond > only to leave two methanes or nothing? > > Regards, > Ralf Stephan > > > > ------------------------------------------------------------------------------ > Got visibility? > Most devs has no idea what their production app looks like. > Find out how fast your code is with AppDynamics Lite. > http://ad.doubleclick.net/clk;262219671;13503038;y? > http://info.appdynamics.com/FreeJavaPerformanceDownload.html > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint |
From: A. H. <ang...@ua...> - 2012-09-28 15:01:52
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> Assume you have ethane on the canvas. Now you click Select > Rectangle and draw a selection rectangle around the first C, > the bond middle not included, so your selection *is practically > the first C. Deletion will leave CH4, and I hope you agree. Yes! > Now draw the rectangle a bit wider such that the bond middle > is included, selecting C *and bond. > 1. What will remain when you delete both? CH4 or nothing? Since I did not cover the other C, I'd expect methane to be left. > 2. Would you expect deleting the bond > only to leave two methanes or nothing? Deleting the bond I would expect to leave two methanes Thanks for your efforts in bringing JCP ahead, Ralf |
From: Ralf S. <ra...@ar...> - 2012-09-28 14:50:25
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Hello, I'm looking for feedback on a use case where I'm not sure what users would expect. As that case results at the moment in an exception I offer you the choice to decide how I'll fix it. H3C---CH3 Assume you have ethane on the canvas. Now you click Select Rectangle and draw a selection rectangle around the first C, the bond middle not included, so your selection *is practically the first C. Deletion will leave CH4, and I hope you agree. Now draw the rectangle a bit wider such that the bond middle is included, selecting C *and bond. 1. What will remain when you delete both? CH4 or nothing? 2. Would you expect deleting the bond only to leave two methanes or nothing? Regards, Ralf Stephan |
From: Egon W. <ego...@gm...> - 2012-09-23 14:17:28
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On Sun, Sep 23, 2012 at 3:58 PM, <ra...@ar...> wrote: > The applet page is at: > http://jchempaint.github.com/EditorApplet.html Thanx. Turns out I actually have IcedTea here :) 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: <ra...@ar...> - 2012-09-23 14:05:50
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Please get jchempaint from http://jchempaint.github.com The applet page is at: http://jchempaint.github.com/EditorApplet.html Ralf Stephan |
From: <ra...@ar...> - 2012-09-23 13:47:59
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On Sun, Sep 23, 2012 at 12:22:23PM +0200, Egon Willighagen wrote: > So, it was missing the .dtd in the archive? Exactly. > I wanted to try it, and went to the JCP homepage... there is a link > there about HTML deployment, which I had hoped would give me a live > applet with the new version, but the server gives a gateway timeout > (504): http://toolserver.org/~ayacop/EditorApplet.html Wikimedia Germany again. It's time to clone that page. |
From: Egon W. <ego...@gm...> - 2012-09-23 10:22:54
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Hi Ralf, On Sat, Sep 22, 2012 at 11:46 AM, Ralf Stephan <ra...@ar...> wrote: > There are two important changes in this JCP release: > > * A fix for a problem affecting the reading of CML files. > This went unnoticed for years because of a buggy test case. > Many thanks to John May for directing my nose to the cause. So, it was missing the .dtd in the archive? > * The applet HTML example now supports OpenJDK. The applet > itself already did, but was called wrongly. The same issue in > icedtea-web isn't fixed, but we received a workaround from > Adam Domurad, thanks very much. Well done! I wanted to try it, and went to the JCP homepage... there is a link there about HTML deployment, which I had hoped would give me a live applet with the new version, but the server gives a gateway timeout (504): http://toolserver.org/~ayacop/EditorApplet.html 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...> - 2012-09-22 09:53:25
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There are two important changes in this JCP release: * A fix for a problem affecting the reading of CML files. This went unnoticed for years because of a buggy test case. Many thanks to John May for directing my nose to the cause. * The applet HTML example now supports OpenJDK. The applet itself already did, but was called wrongly. The same issue in icedtea-web isn't fixed, but we received a workaround from Adam Domurad, thanks very much. Further fixes in testing and of regressions, as well as: #34 click C,H,C while bond button active changes result from C2H6 to CH4 #100 atom buttons should deactivate other mode buttons #39 Applet: manual textual input as in Application #28 default load file format: *.cml;*.smi;*.smiles;*.iupac;*.sdf;*.rxn;*.mol #51 set Save as Image default format Have fun, Ralf Stephan |