Camelia, the Perl 6 bug

IRC log for #cdk, 2009-10-19

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Time Nick Message
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08:05 LillePedro Hi, being  a contractor working closely together with Lars Carlsson in Molndal, Sweden, I need to know how to start JChempaint after building dist jars. :-) /Peter Odéus
08:15 jpansanel moin
08:15 zarah hello jpansanel, you fantastic person you
08:16 jpansanel JChemPaint as an Applet or a standalone Java Application ?
08:26 LillePedro standalone java, please. I've checked out gpox-chempaint and ran "ant dist-all". But I don't know which jar file to execute or in which main method to use...
08:32 LillePedro fyi, my goal is to visualise molecules in a GUI. That's what JChemPaint does, right?
08:43 egonw LillePedro: any reason not to use JChemPaint in Bioclipse for that?
08:43 egonw Lars knows Bioclipse very well...
08:43 egonw and Bioclipse is far more flexible than the JChemPaint application alone
08:44 egonw I stopped working on the last, because of that
08:44 egonw (btw, hi!)
08:53 LillePedro Hi, Egon this Lars.
08:54 egonw hi Lars :) "/nick lars" ?
08:54 LillePedro The reason we want to use jchempaint is that we want to have a lightweight display of reaction pairs for debugging purposes when we generate data for MetaPrint2D.
08:55 LillePedro So basically what we want is a way of calling a method to display two compounds simultaneously and highlight what we call a reaction center.
08:56 egonw ah, ok
08:56 LillePedro Wouldn't jchempaint be more suited for this than Bioclipse?
08:56 egonw depends on the deployment
08:56 egonw but this is possibly with both, indeed
08:57 LillePedro Visual debbuging. To make sure that we identified the correct reaction center.
08:57 egonw I am not entirely sure of the state of IReaction rendering
08:57 egonw but easiest would be to just use two  AtomContainer renderers, side by side
08:57 LillePedro I guess with Bioclipse we get a lot more dependencies that we wouldn't use.
08:57 egonw and use the highlight to mark the reaction center
08:57 egonw yes, likely
08:57 LillePedro Two atom containers would be fine.
08:57 LillePedro Sounds good.
08:58 egonw are the jchempaint application menus important?
08:58 LillePedro not very
08:58 egonw because the application has only one rendering view...
08:58 egonw and you'd have to layout the molecules side by side
08:58 egonw with the *separate* views that would be easier
08:58 LillePedro but, it would be useful to specifiy a reaction id and get the corresponding pair of atoms rendered.
08:59 egonw on the other hand, you probably want to synchronize the zoom and scale then
08:59 LillePedro separate views is ok
08:59 egonw Gpox: if only we had transparent selection marking online yet...
09:00 egonw ok, this is what I would suggest...
09:00 egonw write a simple custom application...
09:00 LillePedro Do you guys think you can assist Peter just a little to get started?
09:00 egonw with a central JPanel split in half
09:00 egonw with two JPanel's...
09:00 egonw from the panel it is easy to get a renderer, to pass to the AtomContainer rendere...
09:01 egonw yes, I guess that should be possible...
09:01 egonw depends a bit on the time line...
09:01 egonw what's his schedule?
09:01 egonw I am rather busy this week
09:01 egonw and on holiday next week
09:01 egonw questions is no problem...
09:01 egonw but hacking up example code is a bit trickier right now...
09:02 LillePedro We can probably figure things out. We just wanted to make sure that we are on the right track and perhaps other people here (#cdk) could answer som questions.
09:03 egonw ok, good
09:03 egonw btw, the jcp application was always started like.
09:03 egonw :
09:03 egonw java -jar jchempaint.jar
09:03 egonw but have not checked if Stefan has changed that, but would find that unlikely...
09:03 LillePedro Peter will be working at AZ for some time. Plz talk to Ola about some of the specifics around this. I dont want to be too explicit in apublic forum.
09:04 egonw no worries
09:04 egonw yes, this channel *is* logged
09:04 egonw and *will* end up in the google caches
09:05 egonw ok, have to go downtown now...
09:05 egonw will be at BMC in about an hour, hour and a half
09:05 LillePedro Ok I'll leave you for now but Peter will be online. See you.
09:05 egonw bye
09:05 egonw LillePedro: Peter, I'll be around after lunch if you have further questions...
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09:47 CIA-29 cdk: mark_rynbeek * r14992 /jchempaint/trunk/build.xml: added obfuscation escape for applet classes
10:26 CIA-29 cdk: shk3 * r14993 /jchempaint/trunk/src/main/org/openscience/​jchempaint/dialog/PeriodicTablePanel.java: there is now an empty space around details in periodic table (bug #10)
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11:14 egonw LillePedro: ping
11:14 egonw LillePedro: I later realized that you are of course not restricted to the Swing widget set...
11:14 egonw you can use SWT too...
11:14 egonw which is also used by Bioclipse...
11:14 egonw that way, the Uppsala team could more easily support you
11:50 Gpox egonw: About transparent selections http://github.com/goglepox/bioclipse.cheminformati​cs/commit/964828448c3a06007db7b854fd7b23a1d953b7e3 :)
11:50 zarah Gpox's link is also http://tinyurl.com/yjnng42
11:50 egonw Gpox++
11:50 egonw got a screenshot?
11:53 LillePedro egonw: I'll consider both Swing and SWT. thanks.
11:54 egonw ok :)
11:57 Gpox egonw: http://img38.imageshack.us​/img38/7793/picture3an.png
11:57 zarah Gpox's link is also http://tinyurl.com/yh7rpfs
11:58 egonw nice...
11:58 egonw there is no option for multiple simultaneous selections yet, right?
11:58 Gpox no
11:58 egonw oh, perhaps I can suggest round shapes for the selection?
12:01 Gpox The Oval selection shape in SelectedAtomGenerator is not filled, possible another rendering parameter 'selectionShapeFilled'
12:01 egonw ok, ok...
12:01 egonw message take...
12:01 egonw yes, yes
12:01 egonw will hurry would this IGeneratorParameter patches :)
12:01 egonw these
12:02 egonw Gpox: http://egonw.posterous.com/arvid-add​ed-support-for-transparent-selection
12:02 zarah egonw's link is also http://tinyurl.com/yhctde2
12:03 egonw Gpox: patch has not shown up in the fork quque yet
12:03 egonw but will apply it asap
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15:36 CIA-29 cdk: shk3 * r14994 /jchempaint/trunk/po/ (3 files in 2 dirs): new russian localization
15:37 CIA-29 cdk: shk3 * r14995 /jchempaint/trunk/src/main/org/openscienc​e/jchempaint/action/CopyPasteAction.java: the paste is pasting mol file as string and smiles and mol file with their mime types
15:55 sneumann joined #cdk
16:06 CIA-29 cdk: shk3 * r14996 /jchempaint/trunk/src/main/org/openscienc​e/jchempaint/action/CopyPasteAction.java: the paste now uses mdl flavor if available, else string with format detection.
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