Camelia, the Perl 6 bug

IRC log for #cdk, 2008-11-26

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All times shown according to UTC.

Time Nick Message
00:06 CIA-16 cdk: gilleain * r13289 /cdk/branches/jchempaint-primary/src/main/org/ope​nscience/cdk/renderer/IntermediateRenderer.java: Provide a natural scale factor lower bound.
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08:47 egonw moin
08:47 zarah hi egonw
09:19 jonalv joined #cdk
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10:17 jbrefort joined #cdk
11:15 gilleain joined #cdk
11:18 gilleain ohai
12:03 jonalv gilleain: oh hai
12:03 gilleain :)
12:04 gilleain http://4.bp.blogspot.com/_eL4nhrOF5R4/SSw7k4UGf​jI/AAAAAAAAAG0/UmVELAel2xY/s1600-h/cdk_city.png
12:04 zarah gilleain's link is also http://tinyurl.com/59yhxr
12:04 jonalv whatäs that?
12:05 gilleain cdk-city!
12:05 gilleain masak sent me a link to the software yesterday.
12:05 jonalv cool
12:05 * jonalv is looking forward to Bioclipse2 city
12:06 gilleain oh, wow. that would be huge. hmmm.
12:06 jonalv yea cdk would be like a suburb... :)
12:08 egonw wow
12:09 egonw gilleain: you got a blog item to that?
12:09 gilleain yup. usual place.
12:09 jonalv where that?
12:10 egonw http://gilleain.blogspot.com/
12:10 gilleain don't think I can make it work with bioclipse very easily, though.
12:11 egonw so, what does the volume describe?
12:11 egonw the size of the class?
12:11 egonw and the blue boxes?
12:11 egonw java packages?
12:11 gilleain mom
12:12 egonw see blog comment
12:12 gilleain this presentation explains:
12:12 gilleain http://www.slideshare.net/wettel/visual-​exploration-of-largescale-system-evoluti​on-presentation-687858?type=powerpoint
12:12 zarah gilleain's link is also http://tinyurl.com/5lz4oj
12:13 gilleain it's well worth flicking through, for the crumbling towers of rapidly changing classes :)
12:13 jonalv gilleain: why would it be difficult with Bioclipse?
12:14 gilleain well, the way I ran it for cdk was from eclipse, and it worked with a single eclipse project.
12:14 gilleain bioclipse is multiple projects (plugins), so it doesn't seem to work.
12:15 gilleain But, I think that there are other (maybe command line) tools to convert code to .mse files.
12:15 egonw ha, Jmol is in that presentation :)
12:15 egonw cool
12:16 egonw among the JDK, Azureus :)
12:17 gilleain yup, I like the bit where all 5 cities are shown in one image, visualising like a million lines of code or more.
12:17 jonalv yea that's cool
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13:52 jonalv is it impossible to calcualte SMILES for a molceule without bonds_
13:53 jonalv (yea that would be just one atom...)
13:53 gilleain makes sense
13:53 gilleain or a group of ions
13:53 gilleain actually, that's ionic bonds, I spose.
13:54 jonalv I donät know how that's modelled...
13:54 egonw C.C.C would be three carbons without bonds
13:54 egonw [Na+].[Cl-]
13:55 jonalv so is there a generalproblem with creating smiles if there are no bonds?
13:55 jonalv because bioclipse does not allow it...
14:03 gilleain egonw: should we have an AddRingModule and an AddBenzeneModule?
14:06 gilleain oh, wait, I've just realised the stack overflow was my fault.
14:08 gilleain no, wait, it wasn't.
14:18 gilleain oh bother.
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17:54 CIA-16 cdk: shk3 * r13320 /jchempaint/trunk/src/main/org/openscience​/jchempaint/action/ChangeModeAction.java: prepared for a lasso module
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20:13 CIA-16 cdk: egonw * r13321 /cdk/branches/jchempaint-primary/src/​main/org/openscience/cdk/controller/ (AddRingModule.java IChemModelRelay.java): Removed duplicate API for adding benzene
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22:36 CIA-16 cdk: gilleain * r13322 /cdk/branches/jchempaint-primar​y/src/main/org/openscience/cdk/ (2 files in 2 dirs): Charge now renders.

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