Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-03

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All times shown according to UTC.

Time Nick Message
00:27 simbot_ joined #cdk
03:19 simbot_ joined #cdk
03:41 CIA-17 cdk: rajarshi * r9816 /trunk/cdk/src/org/openscience/cdk/test​/atomtype/CDKAtomTypeMatcherTest.java: Updated to add a test for the carbon and nitrogen in isonitrile (charge separated form)
03:43 simbot__ joined #cdk
05:42 simbot_ joined #cdk
06:14 thomas_ku joined #cdk
06:14 thomas_ku moin
07:27 CIA-17 cdk: egonw * r9817 /trunk/cdk/src/org/openscie​nce/cdk/io/MDLReader.java: Removed debug line
08:55 steinbeck joined #cdk
08:56 jpansanel moin
08:56 jpansanel moin
08:56 steinbeck moin
09:13 jonalv joined #cdk
09:26 thomas_ku steinbeck: are you already at the ebi?
09:27 steinbeck thomas_ku: no - I go there on Sunday
09:28 thomas_ku So your last days in Germany... enjoy them ;-)
09:29 steinbeck Well, I'll be home a few days every week - thus no real farewell. :-)
09:30 thomas_ku Yeah I thought that!
09:33 egonw joined #cdk
09:33 egonw moin
09:34 steinbeck moin
09:34 steinbeck happy new year
09:34 egonw same here
09:40 jpansanel I've found an intersting conference:
09:40 jpansanel http://www.uom.ac.mu/icce/index.asp
09:40 egonw .mu??
09:40 jpansanel mauritius island ;)
09:41 jpansanel international conference on chemical education
09:41 jpansanel in the ICT age
09:41 dleidert joined #cdk
09:41 jpansanel min daniel
10:05 CIA-17 blueobelisk: pansanel * r237 /structures-html/trunk/index.html: Updating the webpage
10:08 thomas_ku steinbeck: I fear the ebi has written your first name wrong: Or do you have an e at the end? http://www.ebi.ac.uk/Groups/
10:10 jbrefort joined #cdk
10:20 steinbeck thomas_ku: thanks - I'll let them know :-)
10:27 steinbeck egonw: we have been concurrently editing the cdk doc, as I saw now. Hope it worked :-)
10:27 egonw :)
10:27 egonw did not hack it today yet
10:27 steinbeck ack
10:27 egonw added 42 citations for the CDKI and II article yesterday
10:28 egonw working on the summary now
10:28 egonw but nothing in the main doc yet
10:28 egonw will first finish the "CDK Literature #3" blog item
10:28 steinbeck yes, saw that. Thanks
10:49 egonw Book on Jmol: http://stores.lulu.com/angel_herraez
11:02 masak joined #cdk
11:04 * egonw wonders if Christoph is in Hinxton right now...
11:12 thomas_ku egonw: no he will go to Hinxton on sunday!
11:12 egonw ah :)
12:06 steinbeck joined #cdk
12:18 egonw steinbeck: http://chem-bla-ics.blogspot.co​m/2008/01/cdk-literature-3.html
12:19 egonw tommorow I hope to have the follow up, and be up to date again...
12:21 steinbeck This is for re-use in the proposal, I guess :-)
12:23 egonw correct
12:23 egonw and for CDK News :)
12:23 egonw which did not see a issue last year :(
12:23 steinbeck well - we all know why that is
12:24 steinbeck still have to move the cdk news OJS to my steinbeck-molecular server
12:26 egonw and the CDK plone must still be moved too :(
12:27 steinbeck which is a big problem because of the never updated age old plone version on almost
12:27 egonw since the content has not been updated much too, start from scratch?
12:28 steinbeck shouldn't we then try to do without plone - just wikimedia?
12:28 egonw the one on cdk.wiki.sf.net ?
12:28 egonw have been thinking about that too...
12:32 simbot_ joined #cdk
12:32 egonw simbot_: how did the jar from last night do?
12:34 simbot_ not too bad, there were still a few non-percieved atoms, but it worked fine for what i was doing which was aligning outputs from DragonX.
12:34 simbot_ I have a list of the ones which had problems, though I haven't checked it against the old list, so there might not be any new info in it.
12:34 egonw oh, that sounds interesting...
12:35 egonw never done that myself yet...
12:35 steinbeck wow - this is quite an elaborate bot. I just read about another one which passed the Turing test recently.
12:35 egonw are you also going to compare CDK descriptors with the equivalent from Dragon?
12:36 egonw steinbeck: does good ferry tales too... he told yesterday that 4000 SMILES took 4h with CDK 1.0 and about 5 seconds with trunk/ :)
12:36 simbot_ I am going to try. I'm also looking at what mopac(?) can produce.
12:36 steinbeck cool
12:36 egonw steinbeck: yeah, that stupid AllRingsFinder for aromaticity detection comb explosion
12:37 steinbeck now, is that a fairy tale or is that real
12:37 steinbeck ?
12:37 steinbeck if yes, this is very cool
12:37 simbot_ it was real
12:37 steinbeck cool
12:37 steinbeck simbot_: are you from Frankfurt?
12:37 simbot_ no, Australia
12:38 steinbeck ah
12:38 steinbeck almost
12:38 steinbeck :-)
12:43 egonw simbot_: 2004- Nigel Sim PhD Grid computing for data mining of Mass Spectra fingerprinting
12:43 egonw that's you?
12:43 simbot_ maybe :)
12:43 egonw no need to be shy on that project description :)
12:45 * egonw sees a lot of chemometricians down the homepage of Coomans
12:46 egonw is he your promotor?
12:46 simbot_ true, and it'll be all better when it is completed too.
12:47 egonw you got a page on what you do yourself?
12:47 egonw might be quite close to what I did in chemometrics
12:47 simbot_ somewhat, he's my primary supervisor, and he certainly like playing the showman
12:48 simbot_ Um, I don't know if there is anything recent. I've mainly been focusing on the IT end more than the application end, and just collaborating with people in the field.
12:48 simbot_ Most of the rest of coomans students are from stats, I'm from computer science
12:48 egonw sounds good...
12:49 simbot_ what was it you did in chemometrics?
12:49 egonw the group where I did my PhD (Buydens, also hosts the VICIM HQ which Coomans has a cooperation with) doesn't have that sort of IT collaboration
12:49 egonw molecular representation
12:49 egonw in data analysis
12:50 egonw e.g. discussed the use of whole NMR spectra as QSAR/QSPR descriptor
12:50 egonw and crystal structure clustering
12:57 simbot_ ah ok, I can see the similarities to how i started out, except MS not NMR. Do you have a publication on the NMR-QSAR work?
12:57 simbot_ On the use of 1H and 13C NMR spectra as QSPR descriptors, J.Chem.Inf.Model., 2006 ?
12:57 egonw yes
12:57 egonw and you might find my review interesting too
12:57 egonw mom, will look up doi
12:58 egonw 10.1080/10408340600969601
12:59 egonw brb
13:09 simbot_ thanks. fyi these are the remaining smiles http://www.nigelsim.org/not-percieved2.txt
13:10 simbot_ bed time, night
13:13 steinbeck left #cdk
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13:37 CIA-17 bioclipse: jonalv * r4613 /branches/bioclipse2/bioinformatics/​plugins/net.bioclipse.biojava.busine​ss/META-INF/spring/context-osgi.xml: commented out nonworking code for now...
13:42 CIA-17 blueobelisk: pansanel * r238 /structures-tools/trunk/images/ (cd_cover.xcf methionine.xcf): Adding art-work
13:43 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 5015, 78 fails + 58 errors (2.7%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
13:43 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 5015, 78 fails + 58 errors (2.7%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
14:00 CIA-17 bioclipse: carl_masak * r4614 /branches/bioclipse2/ (4 files in 3 dirs): * removed superfluous overrides
14:18 CIA-17 cdk: egonw * r9818 /trunk/cdk/src/org/openscience/cdk/​test/smiles/SmilesParserTest.java: Added another test for charged atoms
14:43 CIA-17 bioclipse: carl_masak * r4615 /branches/bioclipse2/core/plugins/ (10 files in 3 dirs):
14:43 CIA-17 bioclipse: [net.bioclipse.core]
14:43 CIA-17 bioclipse: [net.bioclipse.ui]
14:43 CIA-17 bioclipse: * moved these from core to ui
14:43 CIA-17 bioclipse: ** ConsoleEchoer
14:43 CIA-17 bioclipse: ** EchoListener
14:43 CIA-17 bioclipse: ** EchoEvent
14:51 CIA-17 blueobelisk: pansanel * r239 /structures/trunk/ (12 files in 3 dirs):
14:51 CIA-17 blueobelisk: trunk/tools/*.py: fix html output
14:51 CIA-17 blueobelisk: trunk/AUTHORS: adding more authors
14:51 CIA-17 blueobelisk: trunk/VERSION: switching to 2.1
14:51 CIA-17 blueobelisk: trunk/src/styles/style.css: new style for html
14:51 CIA-17 blueobelisk: trunk/NEWS: updated for the release
14:51 CIA-17 blueobelisk: trunk/README: updated for the release
14:52 jpansanel chemical-structures 2.1 is released
15:59 jpansanel egonw : the link "Web Site" on http://sourceforge.net/projects/bodr/ is broken
16:01 egonw please try again
16:12 CIA-17 bioclipse: egonw * r4616 /branches/bioclipse2/chemoinformatics/net.biocli​pse.cdk.ui/src/org/openscience/cdk/applications/​jchempaint/action/AdjustBondOrdersAction.java: Fixed compile error
16:22 jpansanel egonw : works !
16:22 egonw excellent
16:46 CIA-17 bioclipse: jonalv * r4617 /branches/bioclipse2/core/plugins/ (2 files in 2 dirs): moved the code starting the Spring-extender bundle into an Activaor that always get's runned
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20:10 CIA-17 cdk: egonw * r9819 /trunk/cdk/src/org/openscience​/cdk/graph/SpanningTree.java: Made a local method private and removed an unused method (PathTools.resetFlags is used instead, with the same code)
20:11 CIA-17 cdk: egonw * r9820 /trunk/cdk/src/org/openscience/cdk​/test/graph/SpanningTreeTest.java: Added missing unit tests
20:33 dleidert joined #cdk
20:58 CIA-17 bioclipse: shk3 * r4618 /trunk/plugins/net.bioclipse.specmol/ (2 files in 2 dirs): specmol creation more user friendly

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