Camelia, the Perl 6 bug

IRC log for #cdk, 2007-09-20

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All times shown according to UTC.

Time Nick Message
00:00 Nout hmm
00:01 Nout private Dimension backgroundDimension = new Dimension(794,1123);
00:01 Nout that's the default? odd numbers
00:01 egonw indeed
00:01 egonw no idea where those come from...
00:01 egonw try svn annotate :)
00:01 Nout perhaps an inside joke :)
00:02 egonw anyway...
00:02 egonw got it running...
00:02 egonw in rendering only mode
00:02 Nout cool
00:26 egonw http://chem-bla-ics.blogspot.com/2007​/09/swt-view-with-new-jchempaint.html
00:28 Nout ack
00:31 Nout ah well, really time to go to bed now egonw, will see you tommorrow
00:31 egonw ok, cu
00:32 * Nout wonders how much he'll be able to follow from the college at 9:00 :x
00:33 CIA-31 bioclipse: egonw * r3787 /trunk/playground/plugins/ne​t.bioclipse.cdk.progz/jars/ (cdk-1.0.jar cdk-trunk-20070920.jar): Renamed to make clear that it is not CDK 1.0.
02:25 cpyang joined #cdk
02:40 CIA-31 jmol: hansonr * r8294 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.25 version
06:53 thomas_ku joined #cdk
06:55 thomas_ku moin
07:06 carsten joined #cdk
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07:54 jpansanel moin
08:02 carsten jpansanel: a friend (teacher as well) loves your molecules database :)
08:02 jpansanel carsten : thx :)
08:03 jpansanel tell me if he need anything else
08:03 carsten jpansanel: I see you just added some carboxylic acids and acid anhydrides
08:03 carsten nice to see updates
08:03 jpansanel yes
08:03 jpansanel maleic acid and maleic anhydrides
08:03 jpansanel and fumaric acid also
08:03 carsten hey, I just noticed a missing group...
08:03 carsten sugars...
08:04 jpansanel carbohydrates
08:04 carsten carsten@moinmoin:~/svn/blueobelisk/stru​ctures/trunk/src/carbohydrates> ls
08:04 carsten 2S_3R-butane-1_2_3_4-tetrol.cml  CMakeLists.txt  index.xml
08:04 jpansanel (contains only 1 molecule)
08:05 carsten Glucose 6-(hydroxymethyl)oxane-2,3,4,5-tetrol
08:05 jpansanel it's into my TODO
08:05 carsten is the todo online?
08:05 jpansanel yes
08:05 jpansanel trunk/TODO
08:05 carsten found
08:05 jpansanel Add Carbohydrates (monosaccharides and disaccharides)
08:05 carsten Add Carbohydrates (monosaccharides and disaccharides)
08:05 carsten :)
08:05 jpansanel :)
08:06 CIA-31 blueobelisk: pansanel * r113 /structures/trunk/TODO: remove done work
08:07 carsten jpansanel: if you add ATP you also need to add ADP and AMP
08:08 carsten and also GTP/GDP/GMP (Guanosine-5'-triphosphate ...)
08:08 carsten man, that has also a nice name: 9-β-D-ribofuranosyl-2-amino-​6-oxo-purine-5'-triphosphate
08:10 jpansanel :)
08:10 jpansanel yes it is
08:11 carsten jpansanel: I just went through the files. Sugars and ATP would really by nice. Other than that your database is really complete. Some chiral structures would be nice, but perhaps those are even in there...
08:11 carsten for example, D and L-glucose would be cool
08:12 jpansanel I would add glucose and fructose
08:14 carsten jpansanel: I will demo your database next week
08:14 carsten while demoing Avogadro
08:15 carsten jpansanel: a bit promo never hurts
08:15 jpansanel yes
08:15 jpansanel thx
08:15 carsten jpansanel: I also found some translation issues. I will report them to you, probably today or tomorrow
08:15 carsten ok, need to guy, bye
08:15 jpansanel ok
08:15 jpansanel bye
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08:17 CIA-31 bioclipse: jonalv * r3788 /trunk/playground/plugins/ (16 files in 4 dirs): Added some Copyright text. Not sure about the contributors part so I left it empty for now.
08:18 egonw jonalv: in the contributors part you add yourself...
08:18 CIA-31 bioclipse: jonalv * r3789 /trunk/playground/plugins/net.bioclip​se.structuredb/tests/net/bioclipse/st​ructuredb/domain/StructureTest.java: skeleton implementation of test case
08:19 egonw jonalv: if you start from other source code, you leave the exisiting contributor list intact
08:19 CIA-31 bioclipse: jonalv * r3790 /trunk/playground/plugins/​net.bioclipse.structuredb/ (11 files in 5 dirs): Added some Copyright text. Not sure about the contributors part so I left it empty for now.
08:20 jonalv I have been loking around and I am somewhat confused. Core api would that be Bioclipse core or what?
08:20 jonalv not entirely obvious
08:21 egonw that extra after your name would be some comment on what you added your seelf
08:21 egonw write something like:
08:21 egonw "initial implementation" or "added functionality for X"
08:22 egonw or just put in no comment
08:22 egonw that's fine too
08:22 jonalv Isn't it enough with the @authoer tag in the javadoc?
08:22 jonalv You say I should add my name in authors? oki I'll do that then...
08:24 egonw jonalv: not sure... I think the contributors section is Bioclipse convention... ask Ola
08:25 jonalv will do
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08:41 steinbeck moin
08:41 egonw hi steinbeck
08:41 thomas_ku hi steinbeck
08:43 egonw afk, bbl
09:07 CIA-31 bioclipse: jonalv * r3791 /trunk/playground/plugins/​net.bioclipse.structuredb/ (4 files in 2 dirs): test case double references for Structure works
09:09 Nout yo
09:37 CIA-31 bioclipse: jonalv * r3792 /trunk/playground/plugins/​net.bioclipse.structuredb/ (4 files in 2 dirs): Work on passing test cases in LibraryTest and StructureTest
09:41 jonalv Is it standard precedure in CDK to throw an Exception? Or are there more specific Exception types that should be used instead.? I got a bit suprised when I was supposed to catch an Exception when creating a fingerprint...
09:42 egonw many algorithms throw an exception if incorrect input is passed
09:43 jonalv Shouldn't it throw something more precis like say IllegalArgumentException?
09:45 egonw that's an option no chosen by design
09:45 egonw (feel free to bring it up on the mailing list)
09:45 egonw it could use some new discussion
09:46 jonalv I was just wondering if you had a standard way of doing it... Because I always get a bit confunded when catching an Exception since I strictly speaking can't have any idea of what threw it....
09:47 jonalv Where an Exception in this case means an Exception which is an instance of the base class Exception... :)
09:49 egonw right...
09:50 egonw there are some CDKException's around...
09:50 egonw for special cases...
09:50 egonw but formal conventions forbid that... (now, at least)
09:50 jonalv okey well I was just thinking... (that can be troublesome to do...)
09:57 jonalv Is there a smarts generator in CDK? I can't find it if there is one...
09:59 egonw SMARTS parser, yes... generator not
09:59 egonw going for lunch now
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10:11 CIA-31 bioclipse: jonalv * r3793 /trunk/playground/plugins/net.biocl​ipse.structuredb/src/net/bioclipse/​structuredb/domain/Structure.java: All tests pass for now. Time to extend and write more!
10:21 steinbeck jonalv: we had special exceptions earlier but it turned out to be useless - I think
10:22 jonalv oh? interesting...
10:22 steinbeck I throw a default java.lang.Exception with a nice text why it happened.
10:22 jonalv okey
10:39 CIA-31 bioclipse: jonalv * r3794 /trunk/playground/plugins/net.bioclipse.keyring/ (5 files in 4 dirs): Some copyright texts and made sure jasypt classes are exported
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12:30 CIA-31 jmol: hansonr * r8295 /trunk/Jmol/build.xml: build includes .js files (I think)
12:37 CIA-31 bioclipse: jonalv * r3795 /trunk/playground/plugins/​net.bioclipse.structuredb/ (6 files in 3 dirs): Wrote BaseObjectTest and UserTest
13:16 Nout egonw i'm gone, see ya later!
13:16 egonw ok, cu
13:16 egonw I might not be there before 18:30
13:16 Nout oki
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14:44 CIA-31 bioclipse: jonalv * r3796 /trunk/playground/plugins/​net.bioclipse.structuredb/ (6 files in 2 dirs): All domain tests I currently can figure out to write now passes.
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18:16 CIA-31 jmol: nicove * r8296 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
18:18 CIA-31 jmol: nicove * r8297 /trunk/Jmol-FAH/projects/p3711.xyz.gz: Folding@Home
19:03 CIA-31 jmol: nicove * r8298 /trunk/Jmol-FAH/projects/ (p3304.xyz.gz p3305.xyz.gz): Folding@Home
19:20 CIA-31 jmol: hansonr * r8299 /trunk/Jmol/src/org/jmol/ (6 files in 3 dirs): JmolExportInterface upgrade for Pim
19:49 CIA-31 jmol: hansonr * r8300 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs): for Pim

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