Camelia, the Perl 6 bug

IRC log for #cdk, 2009-02-26

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All times shown according to UTC.

Time Nick Message
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09:53 jpansanel moin
09:53 zarah hello jpansanel, you fantastic person you
09:57 egonw hi jpansanel
10:07 CIA-62 cdk: egonw * r14264 /cdk/branches/jchempaint-primary/src/main/org/open​science/cdk/controller/ControllerParameters.java: Removed hydrogen (solving the atom to 'disappear' when explicit hydrogen are supressed) and added halogens
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11:54 CIA-62 cdk: shk3 * r14265 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (ControllerHub.java IChemModelRelay.java): improved api
12:02 CIA-62 cdk: shk3 * r14266 /jchempaint/trunk/ (4 files in 3 dirs): pressing delete now deletes selection
12:24 CIA-62 cdk: shk3 * r14267 /jchempaint/trunk/src/main/org/opensci​ence/jchempaint/JChemPaintPanel.java: when atom is highlighted, symbol can easily be changed by typing symbols
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12:33 de__maas egonw: around?
12:34 egonw hi de__maas
12:34 de__maas HI how's life?
12:34 egonw good :)
12:34 egonw Uppsala is nice
12:34 egonw I was just educated in the blood-brain barrier
12:34 de__maas I should come up with a excuse to visit you there
12:35 de__maas Ah, that nice stuff.
12:35 de__maas Would be nice to have descriptor
12:35 egonw yes, you would be welcome, of course...
12:35 egonw to make BBB models?
12:36 de__maas Yep, not sure if there is a good one available but could be very interesting
12:36 de__maas I've a question about the mdIteratorReader.
12:36 egonw well, there seem to be several passive and active mechanism at work...
12:37 egonw hard to model in one model, I guess...
12:37 egonw yes, what about the MDLIterReader?
12:37 de__maas true, it's not an easy task
12:37 de__maas I noticed you fixed the bug with the Deuterium (and more) entries.
12:37 egonw yes
12:38 de__maas However, Not sure how to capture them because my apps still just stop at those entries.
12:38 egonw if in RELAXED mode, it will handle those
12:38 egonw umm...
12:38 egonw let me check
12:38 de__maas aha were to set the mode?
12:38 egonw constructor
12:38 egonw but relaxed is thed efault
12:39 de__maas I just downloaded the 1.1.5 version is that the right one?
12:39 egonw yes
12:40 egonw I hope to release 1.2.0 next week
12:40 de__maas Cool a lot of work has been done I noticed.
12:41 egonw yes
12:41 de__maas Anyway, I tried Rajarshi app for descriptors and it also stops at the Deuterium entries. Do we need to capture and exception or something?
12:41 egonw no, that should be ok...
12:42 de__maas Hmmm so do you have a suggestion were to look?
12:43 egonw you could email me the troublesome entry offline...
12:44 egonw interpretHydrogenIsotopes = new BooleanIOSetting("InterpretHydrogenIsotopes", IOSetting.LOW,
12:44 egonw "Should D and T be interpreted as hydrogen isotopes?",
12:44 egonw "true");
12:44 egonw that's the used code...
12:44 egonw and it defaults to true
12:50 de__maas Looks very usefull, I noticed the bioclipse 2 release is working OK so the code should be OK I guess.
12:51 egonw indeed
12:51 egonw but the BC2 is using a custom SD reader...
12:51 de__maas OH, so that does not compare then.
12:51 egonw if you used the SDFEditor, no, indeed not...
12:52 de__maas BTW, works very nice this SDFEditor.
12:52 egonw Gpox is working on an even better one...
12:53 egonw which should be part of beta3 due tomorrow
12:53 de__maas It would be even better if you can change the column widths because now you can not read the data in the columns
12:53 egonw :)
12:53 egonw that's exactly a think he fixed in the new beta :)
12:54 egonw de__maas: please feel more than welcome to submit enhancement requests at bugs.bioclipse.net
12:54 de__maas go go gpox :-D
12:54 de__maas Yeah I will but I just returned from holidays so I'm a bit busy.
12:54 egonw :)
12:54 egonw yes, I know that...
12:55 egonw ... problem
12:55 egonw makes holidays be like a problem, as they pile up work you have to do later
12:56 de__maas true, but it's not to bad since I'm not involved in any production process. Currently no deadlines so I cannot complain.
12:57 de__maas I'll first take another look at my code and if I cannot get it to work I will send you some problem entries OK?
12:57 egonw ok
13:17 CIA-62 cdk: shk3 * r14268 /jchempaint/trunk/src/main/org/openscience/​jchempaint/resources/userhelp_jcp/contain/ (keyboard.html molecules.html referenceGuide.html): worked a bit on the help, more will follow
13:21 CIA-62 cdk: shk3 * r14269 /jchempaint/trunk/src/main/org/o​penscience/jchempaint/resources/ (JCPGUI_applet.properties JCPGUI_stable.properties): small cleanup
13:29 * egonw is moving to a different room
13:29 egonw bbl
15:51 CIA-62 cdk: shk3 * r14270 /jchempaint/trunk/src/main/org/openscie​nce/jchempaint/resources/userhelp_jcp/ (28 files in 2 dirs): worked on the help. cleanup up links, made sure all pages are linked etc. Content still needs checking.
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