Camelia, the Perl 6 bug

IRC log for #cdk, 2008-08-11

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All times shown according to UTC.

Time Nick Message
05:03 jbrefort joined #cdk
05:05 bag joined #cdk
07:19 malick joined #cdk
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08:13 egonw joined #cdk
08:37 CIA-34 cdk: egonw * r11983 /cdk/trunk/src/ (57 files in 10 dirs): Moved the CDKAtomTypeMatcher and general purpose helper classes to core
08:43 CIA-34 cdk: egonw * r11984 /cdk-qa/trunk/projects/080808-0001/ (. README diff.bsh): Added tool to give better overview of what goes wrong
08:47 CIA-34 cdk: egonw * r11985 /cdk-qa/trunk/projects/080808-0001/debug.bsh: Added util to find interesting ZINC entries
09:20 jpansanel moin
09:20 zarah hi jpansanel
09:31 CIA-34 cdk: egonw * r11986 /cdk-qa/trunk/projects/080808-0001/README: Added extra info: # of failing ZINC structures, missing cmd line run
09:42 malic1 joined #cdk
09:47 CIA-34 cdk: egonw * r11987 /cdk/trunk/src/main/org/openscien​ce/cdk/dict/data/atom-types.owl: Added missing broader relation
10:03 malic1 joined #cdk
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10:15 thomas_ku joined #cdk
10:15 thomas_ku moin
10:15 zarah hi thomas_ku
10:24 CIA-34 cdk: egonw * r11988 /cdk/trunk/src/ (4 files in 3 dirs): Added perception + Sybyl mapping of new atom types: O.minus.co2 and O.sp2.co2
11:30 egonw anyone here with OB 2.2 running?
14:03 CIA-34 cdk: egonw * r11991 /cdk/trunk/src/META-INF/ (atomtype.datafiles core.datafiles extra.datafiles): Correct distribution of dict/data/*.owl files over the modules (closes #2045603)
14:18 CIA-34 cdk: egonw * r11992 /cdk/trunk/src/ (2 files in 2 dirs): Added aromaticity perception, to support C.ar
14:24 CIA-34 cdk: egonw * r11993 /cdk/trunk/src/META-INF/atomtype.cdkdepends: Grmph... I know it was going to depend on this, and still I forgot to add it :(
14:33 CIA-34 cdk: egonw * r11994 /cdk/trunk/src/main/org/openscience/cd​k/atomtype/SybylAtomTypeMatcher.java: Another Sybyl atom type that includes aromaticity
14:48 rguha joined #cdk
14:48 rguha hi
14:48 zarah hi rguha
14:48 rguha zarah: hi zarah
14:48 zarah hello rguha :)
14:48 rguha zarah: how are you?
14:48 zarah rguha: eh... wha'?
14:52 egonw hi rguha
14:52 rguha egonw: hi
14:52 egonw the bot is not very smart
14:53 rguha egonw: just playing with her :)
14:53 egonw but good for keeping messages
14:53 rguha btw, have you seen, Google is now testing out hosting for research datasets
14:55 egonw no, have not seen that...
14:55 egonw that sounds interesting...
14:55 egonw URL?
14:55 egonw btw, just posted a message to CCL
14:56 egonw about sybyl atom types
14:56 rguha http://research.google.com/
14:56 rguha sorry
14:56 rguha http://research.google.com/datasets/
14:56 zarah rguha's link is also http://tinyurl.com/5dgp83
14:56 rguha as an example http://research.google.com/​datasets/id/grd20080800129
14:56 zarah rguha's link is also http://tinyurl.com/63lsln
14:57 rguha i'll putting up conformers (for the project with JCB) there soon
14:57 egonw I get redirected to google.nl :(
14:57 rguha re: Sybyl types - thanks for that
14:57 egonw yeah, it's shaping up
14:57 egonw found 2 OB bugs :)
14:57 rguha yes, it's not totally public yet I think
14:57 rguha saw those :)
14:58 egonw N.am is rather fuzzy too
14:58 rguha btw, build is broken
14:58 egonw oh...
14:58 rguha atomtype module can't find CDKHueckelAromaticity
14:58 egonw [16:24] <CIA-34> cdk: egonw * r11993 /cdk/trunk/src/META-INF/atomtype.cdkdepends: Grmph... I know it was going to depend on this, and still I forgot to add it :(
14:58 egonw should work
14:59 egonw ah, not
14:59 egonw guess I forgot to do the clean dist-all :(
15:00 egonw crap
15:00 egonw build order :(
15:00 rguha hmm
15:00 rguha ant sometimes gets on my nerves
15:01 egonw yeah, I have an idea on how to do this properly...
15:01 egonw but will postpone that for the NIH grant :)
15:01 egonw should write that idea up for the proposal though...
15:01 egonw crap... too few hours per day :(
15:02 rguha ha - need to slow the earth :)
15:02 egonw I need slaves^WPhD students
15:02 rguha :)
15:02 rguha did you check in a fix? doesn't build yet
15:02 egonw btw, make olas happy, join #bioclipse too
15:03 egonw or are you via a website on IRC?
15:03 rguha one sec
15:06 rguha done
15:06 egonw noted
15:07 egonw olas seems afk :(
15:07 rguha np
15:14 egonw ok, build.xml fix commited
15:14 egonw the CIA is a bit slow this afternoon
15:24 rguha does it build for you? a clean dist-all doesn't work for me (rev 11995)
15:25 egonw yes it did
15:27 egonw what error does it give?
15:27 egonw for which task?
15:27 rguha atomtype module doesn't compile
15:28 rguha same problem as before
15:28 egonw which target?
15:28 rguha ah, sorry
15:28 rguha my fault
15:28 egonw phew...
15:28 egonw ok, got to go in a few minutes...
15:29 rguha ko, bye
15:30 egonw will hack in S.one on the train home
15:30 egonw matching S.O2 in Sybyl
15:30 egonw aromaticity is an obstable...
15:31 rguha hmm
15:31 egonw I think OB and CDK will disagree on what is aromatic
15:31 rguha that is not surprising
15:31 egonw not on all
15:31 egonw ok, will be online tonite
15:31 rguha why? OB and CDK don't use the same aromaticity model (or do they?)
15:31 egonw got to run now
15:31 egonw no, don't think so
15:31 rguha bye
15:31 egonw there is no one aromaticity model
15:31 egonw hueckel
15:31 rguha right
15:31 rguha so I think lots of toolkits disagree with each other
15:32 egonw but the hueckel only applies to single rings...
15:32 egonw or defined for...
15:32 egonw does not say anything about fused things...
15:32 rguha right
15:32 egonw AFAIK
15:32 egonw so, that's where the mess starts :)
15:32 egonw ok, cu later !
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17:05 CIA-34 cdk: egonw * r11996 /cdk/trunk/src/META-INF/atomtype.datafiles: Fixed paths: should not include src/main
17:07 CIA-34 cdk: egonw * r11997 /cdk/trunk/src/test/org/openscience/cdk​/atomtype/CDKAtomTypeMatcherTest.java: Added two test cases
17:16 CIA-34 cdk: egonw * r11998 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Take the OB approach: ring nitrogens can be amides too
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