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From: Stefan Kuhn <stefan.kuhn@eb...> - 2008-06-19 10:15:34
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On Thursday 19 June 2008 10:36:45 Christoph Steinbeck wrote: > Egon, > > extremely useful information indeed! > > One remark: We *really* need to get rid of the name > "GeometryToolsInternalCoordinates". > In Chemoinformatics and Computational Chemistry, as you and everyone > else here know of course, Internal Coordinates mean something very > different, namely the representation of a molecules geometry by means of > bond length, bond angles and dihedrals. Not everyone else - I didn't, obviously, I wouldn't have named them like this. > May I suggest renaming this class to something like > GeometryToolsDVICoordinates, with DVI standing for "DeViceIndepent". ?????? > I wonder anyway, why we need two different classes for these Geometry > Operations. Well, the original class was/is for manipulating Point2ds. Since this was used in several places, I left it and made a new class using the "internal coordinates", i. e. the one in the RendererModel. To get rid of a class, we need to get rid of its use. The "internal coordinates" one should be no longer necessary with using Java2D and the new renderer, shouldn't it? Stefan |
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From: Egon Willighagen <egon.willighagen@gm...> - 2008-06-19 10:03:13
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On Thu, Jun 19, 2008 at 11:53 AM, Christoph Steinbeck <steinbeck@...> wrote: > Ah, sorry. I just studied your no-longer-applicable blueprint document which > says "Replace the GeometryTools with GeometryToolsInternalCoordinates". > Good to know that this is no longer valid :-) Forgot to mention that in those blue prints, they 'grey' tasks are done. Not very clearly visible. Sorry about that. Egon -- ---- http://chem-bla-ics.blogspot.com/ |
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From: Christoph Steinbeck <steinbeck@eb...> - 2008-06-19 09:53:45
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Egon Willighagen wrote: > On Thu, Jun 19, 2008 at 11:36 AM, Christoph Steinbeck > <steinbeck@...> wrote: >> One remark: We *really* need to get rid of the name >> "GeometryToolsInternalCoordinates". > > Removed some time ago from trunk already. > > All your comments are no longer applicable; not to trunk anyway... > never mind CDK 1.0.x. Removing it there is impossible, but a rename > could be done. People should use trunk, I think, and make a release > soon, and keep CDK 1.0.x just for JCP 2.3.x until JCP 3 comes out. Ah, sorry. I just studied your no-longer-applicable blueprint document which says "Replace the GeometryTools with GeometryToolsInternalCoordinates". Good to know that this is no longer valid :-) Cheers, Chris -- Dr. Christoph Steinbeck Head of Chemoinformatics 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.. |
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From: Egon Willighagen <egon.willighagen@gm...> - 2008-06-19 09:41:58
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On Thu, Jun 19, 2008 at 11:36 AM, Christoph Steinbeck <steinbeck@...> wrote: > One remark: We *really* need to get rid of the name > "GeometryToolsInternalCoordinates". Removed some time ago from trunk already. All your comments are no longer applicable; not to trunk anyway... never mind CDK 1.0.x. Removing it there is impossible, but a rename could be done. People should use trunk, I think, and make a release soon, and keep CDK 1.0.x just for JCP 2.3.x until JCP 3 comes out. Egon -- ---- http://chem-bla-ics.blogspot.com/ |
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From: Christoph Steinbeck <steinbeck@eb...> - 2008-06-19 09:36:58
|
Egon, extremely useful information indeed! One remark: We *really* need to get rid of the name "GeometryToolsInternalCoordinates". In Chemoinformatics and Computational Chemistry, as you and everyone else here know of course, Internal Coordinates mean something very different, namely the representation of a molecules geometry by means of bond length, bond angles and dihedrals. May I suggest renaming this class to something like GeometryToolsDVICoordinates, with DVI standing for "DeViceIndepent". I wonder anyway, why we need two different classes for these Geometry Operations. We should open this problem here for discussion. Cheers, Chris Egon Willighagen wrote: > All, > > A further JCP update, > > On Mon, May 12, 2008 at 8:47 AM, Egon Willighagen > <egon.willighagen@...> wrote: >> First, I have updated the status report on LaunchPad: >> >> https://blueprints.launchpad.net/cdk/+spec/jchempaint-3.x-release > > OK, the current action point is: > > https://blueprints.launchpad.net/cdk/+spec/cleanup-old-jchempaint-code > > There is old renderer code in trunk/, which I'll remove shortly. > >> where you can see that trunk/ is about cleared from old renderer and >> controller code, and that I am about ready start writing new Swing- >> and SWT-based editor widgets. > > This basically qualifies the steps just after removing all old renderer code: > > 1. define a module renderer API > > this allows plugging in and out certain functionality... Some of which > may require larger CDK modules. The most basic JCP will be mean and > lean... > > Focus from then on, will likely be on a Swing applet and a SWT component. > > 2. port of rendering functionality to the new APIs > > This is a big blob of work. The current renderer does not do much yet, > really, other than visible from Niels' blog: > > http://progz-jchem.blogspot.com/ > > 3. set up a org.openscience.cdk.jchempaint RCP bundle for the SWT widget in: > > http://cdk.svn.sourceforge.net/viewvc/cdk/jchempaint-swt/ > > 4. set up a JCP Swing application in: > > http://cdk.svn.sourceforge.net/viewvc/cdk/jchempaint/ > > (see this blog, > http://chem-bla-ics.blogspot.com/2008/05/development-of-new-jchempaint.html) > > 5. set up a JCP Swing applet in: > > http://cdk.svn.sourceforge.net/viewvc/cdk/jchempaint-applet/ > > Egon > -- Dr. Christoph Steinbeck Head of Chemoinformatics 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.. |