Camelia, the Perl 6 bug

IRC log for #cdk, 2007-11-20

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All times shown according to UTC.

Time Nick Message
04:10 CIA-16 jmol: hansonr * r8640 /trunk/Jmol/src/org/jmol/modelsetbio/ (NucleicMonomer.java PhosphorusMonomer.java): version=11.3.46_dev # bug fix: tRNA, rRNA with abnormal distances do not connect biopolymers
06:53 egonw joined #cdk
07:18 egonw LaserJock: just read this post: http://stompbox.typepad.com/blo​g/2007/11/mantha-on-the-m.html
07:19 egonw go LaserJock
07:19 egonw :)
07:24 LaserJock lol
07:25 egonw :)
07:55 thomas_ku joined #cdk
07:56 thomas_ku moin
07:56 egonw hi thomas_ku
07:57 thomas_ku hi egonw
08:27 egonw thomas_ku:
08:27 egonw Exception in thread "Update Repository Progress" java.lang.ExceptionInInitializerError
08:27 egonw at org.openscience.cdk.applications.t​averna.scuflworkers.cdk.CDKScaveng​er.<clinit>(CDKScavenger.java:72)
08:27 egonw at sun.reflect.NativeConstructorAc​cessorImpl.newInstance0(Native Method)
08:27 egonw at sun.reflect.NativeConstructorAccessorImpl.newI​nstance(NativeConstructorAccessorImpl.java:57)
08:27 egonw at sun.reflect.DelegatingConstructorAccessorImpl.newI​nstance(DelegatingConstructorAccessorImpl.java:45)
08:27 egonw with Taverna 1.6.1 and CDK-T 0.4.0
08:27 thomas_ku egonw: what have you done?
08:28 egonw no idea
08:28 egonw boot taverna :)
08:28 egonw did an update... maybe it has dissappeared now
08:28 thomas_ku ok you did an update to which taverna version?
08:29 egonw ah, install the CDK-T plugin
08:29 egonw 1.6.1 + update...
08:29 egonw mom
08:29 egonw 1.6.1.1
08:31 thomas_ku My cdk-taverna version 0.4.0.0 works with the tav version 1.6.1.1
08:31 thomas_ku did you restart taverna?
08:33 thomas_ku otherwise switch to taverna 1.6.2.1 and to cdk-taverna 0.4.1
08:36 egonw will do
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08:38 thomas_ku this would be the latest version (more or less an inoffical one)
08:39 egonw same update site for the cdk plugin
08:40 thomas_ku yes its the same site
08:40 thomas_ku cdk-taverna.de/plugin
08:40 thomas_ku oh i think the www is missing
08:54 egonw away for coffee
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09:22 rojasm2 hi all
09:22 thomas_ku hi rojasm2
09:23 rojasm2 hi thomas_ku
09:47 jpansanel moin
12:24 masak joined #cdk
13:42 egonw rojasm2: around?
13:58 CIA-16 bioclipse: ospjuth * r4301 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (5 files in 5 dirs): Removed deps on CDK and prepared for Jmol API.
14:11 sneumann joined #cdk
14:12 egonw hi sneumann
14:12 egonw did you register to the ML yet?
14:12 egonw I'm about to do that
14:12 egonw Jan has a question about sepgsql
14:13 sneumann Have patience with an old man, last time I used some kind of chat was back in 1994.
14:13 egonw :) sorry
14:13 sneumann Yes, subscribed to both MLs
14:14 sneumann We have an installation of an earlier release of SEpgsql in a fedora VMware image. I could share that, though a clean install with a current version would make more sense.
14:15 sneumann There are a view PDF slides on their site. If your acroread has problems with the .jp fonts, I have a translated copy.
14:17 egonw I asked Jan to post the question he had on the devel ML
14:31 CIA-16 bioclipse: ospjuth * r4302 /branches/bioclipse2/core/plugi​ns/net.bioclipse.ui/plugin.xml: Updated extension for PDBEditor to .pdb2 to be compatible with new JmolEditor.
14:44 CIA-16 bioclipse: ospjuth * r4303 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (3 files in 3 dirs): Got the JmolEditor working for PDB files. Uses a String as model, and calls JmolViewer.openStringInline(content) to populate Jmol.
14:47 CIA-16 jmol: hansonr * r8641 /trunk/Jmol/src/org/jmol/ (13 files in 5 dirs):
14:47 CIA-16 jmol: version=11.3.46_dev # new feature: calculate polymers
14:47 CIA-16 jmol: # allows recalculation of polymers after connections are made/broken
15:02 CIA-16 cdk: egonw * r9465 /branches/egonw/remove-non-cdkatomtype-co​de/src/org/openscience/cdk/qsar/descripto​rs/molecular/LargestChainDescriptor.java: No need to use the AllRingsFinder anymore.
15:13 CIA-16 cdk: egonw * r9466 /branches/egonw/remove-non-cdkatomtype-code/​src/org/openscience/cdk/qsar/descriptors/mol​ecular/RotatableBondsCountDescriptor.java: No need to use the AllRingsFinder there either.
15:19 thomas_ku joined #cdk
15:25 egonw LaserRock: please ask the ORTEP friend to send an example CIF file with ORTEP info, and a screenshot of what he expects it too look like... e.g. using PLATON
15:25 egonw cu tomorrow
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15:27 CIA-16 cdk: egonw * r9467 /branches/egonw/remove-non-cdkatomtype-​code/src/org/openscience/cdk/qsar/descr​iptors/molecular/XLogPDescriptor.java: One other unneeded use of AllRingsFinder.
15:34 CIA-16 cdk: rajarshi * r9468 /trunk/cdk/src/org/openscience/cdk/test/ (2 files in 2 dirs): Added test case for the AlogP descriptor and update the descriptor module test suite
15:51 CIA-16 cdk: rajarshi * r9469 /trunk/cdk/src/org/openscience/c​dk/tools/AtomicProperties.java: Updated path to the data file, cleaned and simplified the code. Also added to the qsar module, since this is the only current module that makes use of this class
16:22 CIA-16 bioclipse: ospjuth * r4304 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.jmol/ (6 files in 5 dirs): Updated to latest Jmol.jar, head on v20071120, towards 11.4 release. Also refactored methods in JmolPanel.
16:26 CIA-16 bioclipse: ospjuth * r4305 /branches/bioclipse2/chemoinformatic​s/net.bioclipse.jmol/jars/Jmol.jar: Updated to latest Jmol.jar, head on v20071120, towards 11.4 release.
16:30 CIA-16 cdk: rajarshi * r9470 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Update the AlogP descriptor with the code provided by Nina and Nick, which now correctly evaluates the descriptor. Also updated the EState atom type matcher to correctly match the required atom types
16:31 carsten_ joined #cdk
16:32 CIA-16 cdk: rajarshi * r9471 /trunk/cdk/src/META-INF/qsar.datafiles: Updated the data file dependencies for the qsar module to include the whim weights file
16:43 CIA-16 bioclipse: ospjuth * r4306 /branches/bioclipse2/core/​plugins/net.bioclipse.ui/ (bioclipse.product plugin.xml): Moved progress bar down and changed msg color to one with better contrast.
16:48 CIA-16 bioclipse: carl_masak * r4307 /branches/bioclipse2/core/p​lugins/net.bioclipse.core/ (8 files in 4 dirs):
16:48 CIA-16 bioclipse: [net.bioclipse.core]
16:48 CIA-16 bioclipse: * groovy support
16:48 CIA-16 bioclipse: * groovy console
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19:31 CIA-16 jmol: hansonr * r8642 /trunk/Jmol/src/org/jmol/ (5 files in 4 dirs): version=11.3.46_dev # bug fix: color bonds CPK not working
19:41 carsten joined #cdk
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