Camelia, the Perl 6 bug

IRC log for #cdk, 2008-04-01

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
03:07 jpansanel joined #cdk
03:23 bhwu joined #cdk
03:23 bhwu left #cdk
05:35 jbrefort joined #cdk
07:17 masak joined #cdk
08:04 jonalv joined #cdk
08:40 de_maas joined #CDK
09:25 tjeerd joined #cdk
11:19 egonw joined #cdk
11:19 egonw moin
11:19 * egonw won't be online long...
11:21 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 5872, 72 fails + 44 errors (3.51%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk
11:21 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 5872, 72 fails + 44 errors (3.51%) | CDK 1.0.x TODO: see http://cdk.sf.net/wiki/ | Logs at http://moritz.faui2k3.org/​irclog/out.pl?channel=cdk | CDK News paper online on pharmacophores
12:33 carsten joined #cdk
13:10 CIA-20 bioclipse: carl_masak * r5301 /bioclipse/trunk/plugins/net.bioclipse.base2/ (7 files in 3 dirs):
13:10 CIA-20 bioclipse: * adding icons to tree view
13:10 CIA-20 bioclipse: * amazing how visual touch-ups such as this
13:10 CIA-20 bioclipse:  affect the overall look of things
13:10 CIA-20 bioclipse: * this introduces the first dependency on
13:10 CIA-20 bioclipse:  net.bioclipse.core, btw, so base2 is now
13:10 CIA-20 bioclipse:  officially a bioclipse 2 plugin
13:13 jpansanel moin
13:24 carsten Moin Rejoem
13:24 carsten almost, again:
13:24 carsten Moin Jerome
13:24 CIA-20 bioclipse: carl_masak * r5302 /bioclipse/trunk/plugins/net.bio​clipse.base2/icons/datafile.gif: * added icon for data files
13:44 CIA-20 bioclipse: jonalv * r5303 /bioclipse2/trunk/plugins/ (26 files in 8 dirs):
13:44 CIA-20 bioclipse: StructureDB compiles and a few but not all tests passes. The tests that fails
13:44 CIA-20 bioclipse: need the applicationContext.xml which from now on is in META-INF but I can't
13:44 CIA-20 bioclipse: figure out how to reach it when running the tests. If you have any ideas please
13:44 CIA-20 bioclipse: help!
13:48 CIA-20 bioclipse: carl_masak * r5304 /bioclipse/trunk/plugins/net.bioclipse.base2/s​rc/net/bioclipse/base2/db/Base2Database.java:
13:48 CIA-20 bioclipse: * turns out assays without array designs tried to
13:48 CIA-20 bioclipse:  show them regardless of whether they existed or not
13:48 CIA-20 bioclipse: * this resulted in a NullPointerException
13:48 CIA-20 bioclipse: * fixed that
13:58 CIA-20 bioclipse: jonalv * r5305 /bioclipse2/trunk/plugins/ (8 files in 7 dirs): Cleaned up imports
14:07 stika2008 joined #cdk
14:07 stika2008 hell everybody
14:07 stika2008 I'm gianfranco
14:07 carsten I am Carsten
14:07 carsten :)
14:08 stika2008 Egon around?
14:08 stika2008 ciao Carsten
14:08 carsten stika2008: I hope you are not really wishing us to hell, stika2008? :-)
14:08 carsten stika2008: he hasn't been here in the last couple of hours
14:09 stika2008 did you read the last cdk-user emails about the problem with the SmilesGenerator?
14:09 carsten nope, I didn't
14:26 egonw joined #cdk
14:26 stika2008 hi Egon
14:27 stika2008 stika2008 == Gianfranco
14:27 stika2008 stika2008.equals(Gianfranco) == True
14:27 egonw hi stika2008
14:29 stika2008 thanks for the last email, I solved that issue, but still it remains the problem with the generator.
14:30 stika2008 If I build a byphenil with the MoleculeFactory, then I use percieveAtomTypesAndConfigerAtoms and CDKHueckelAromaticityDetector, the bond orders are correct, but
14:30 stika2008 the SmilesGenerator still returns a SMILES with double bonds.
14:30 egonw but then you the MFactory explicitly defined the bond orders
14:31 stika2008 yes
14:31 stika2008 this was just a test
14:32 stika2008 what I'm trying to do is to print out the SMILES (or Inchis) of all the rings for a given molecule
14:33 egonw if you use setUseAromaticityFlag(boolean), does it then do what you like to do?
14:33 egonw could be a temp solution...
14:33 egonw boolean = true;
14:33 stika2008 let me try
14:33 egonw stika2008: sorry, but got to go offline again (and prepare for http://chem-bla-ics.blogspot.com/2008/04/t-​minus-26-hours-defending-open-source.html)
14:34 stika2008 ok, thanks
14:34 egonw will be back online on Thursday
14:34 stika2008 ok!
14:34 egonw we'll have a mini CDK unconference thingy here in Nijmegen...
14:34 stika2008 thanks a lot
14:34 egonw I'll likely be online part of the day...
14:34 stika2008 left #cdk
15:15 CIA-20 bioclipse: jonalv * r5306 /bioclipse2/trunk/plugins/net.bioclipse.stru​cturedb/src/net/bioclipse/structuredb/busine​ss/AbstractDaoBasedStructuredbManager.java: white spaces
16:16 CIA-20 bioclipse: rklancer * r5307 /bioclipse2/trunk/ (2 files in 2 dirs):
16:16 CIA-20 bioclipse: fixes to make StructureDB build (for me): added newly-required Spring plugins to
16:16 CIA-20 bioclipse: target platform and removed of Java 1.5-incompatible @Overrides (can't declare
16:16 CIA-20 bioclipse: @Override for method declared in interface but not superclass)
16:45 jbrefort joined #cdk
17:43 CIA-19 joined #cdk
20:06 jbrefort joined #cdk

| Channels | #cdk index | Today | | Search | Google Search | Plain-Text | summary