Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-16

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Time Nick Message
00:26 CIA-31 cdk: dleidert * r144 /trunk/chemical-mime-data/ (3 files in 3 dirs):
00:26 CIA-31 cdk: 2007-10-16 Daniel Leidert <daniel.leidert@wgdd.de>
00:26 CIA-31 cdk:  * xsl/cmd_gnome-keys.xsl (cm:icon, fdo:comment): Fixed output format.
00:26 CIA-31 cdk:  * src/chemical-mime-database.xml.in: Simple typo fix in the DTD
00:26 CIA-31 cdk:  description.
00:29 CIA-31 jmol: hansonr * r8435 /trunk/Jmol/src/org/jmol/ (4 files in 3 dirs): 11.3.33 bug fix: insertion codes stored incorrectly in 11.3.32
02:12 CIA-31 jmol: hansonr * r8436 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Jmol.properties): version=11.3.33_dev # adds support for "xx'" atom designations in PDB
02:18 CIA-31 jmol: hansonr * r8437 /trunk/Jmol/src/org/jmol/viewer/Compiler.java: version=11.3.33_dev # adds support for "xx'" atom designations in PDB
03:37 CIA-31 jmol: hansonr * r8438 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: (log message trimmed)
03:37 CIA-31 jmol: 11.3.33 Version
03:37 CIA-31 jmol: # adds support for "xx'" atom designations in PDB
03:37 CIA-31 jmol: # bug fix: insertion codes stored incorrectly in 11.3.32
03:37 CIA-31 jmol: # new feature: inline scripting allows math
03:37 CIA-31 jmol: #
03:37 CIA-31 jmol: # script INLINE "select " + site_list[2]
04:51 thomas_ku joined #cdk
04:52 thomas_ku moin
05:59 carsten joined #cdk
06:21 rojasm joined #cdk
06:21 rojasm moin
06:28 egonw moin
06:43 CIA-31 cdk: thomaskuhn * r9086 /trunk/cdk-taverna/src/main/java/org/openscience​/cdk/applications/taverna/CDKTavernaConfig.java: Added a MoleculeID string to the config
06:43 egonw thomas_ku: got a sec?
06:44 thomas_ku egonw: yes
06:44 egonw you asked about a new CDK release, right?
06:44 thomas_ku yes did that!
06:45 thomas_ku I already tried the cdk-1..0.2.pre
06:45 egonw ok, good :)
06:46 thomas_ku So far I got no problem with it!
06:46 egonw good
06:46 egonw there should be some good improvements too...
06:47 egonw e.g. SDG should be much better now
06:47 thomas_ku But I couldn't try to compile it with java 1.4 because I haven't installed it anymore
06:47 egonw same here :(
06:47 egonw OK, got to go to a meeting now
06:47 egonw bbl
06:47 egonw (with my new laptop :)
06:48 thomas_ku yes the sdg should be better! but didn't tied it up to now! I tried it with the trunk version recently and there it was much better!
06:48 thomas_ku you are a lucky man
06:50 CIA-31 cdk: thomaskuhn * r9087 /trunk/cdk-taverna/src/main/java/org/openscien​ce/cdk/applications/taverna/CMLChemFile.java: Removed an import
06:50 CIA-31 cdk: thomaskuhn * r9088 /trunk/cdk-taverna/src/main/java/org/openscienc​e/cdk/applications/taverna/LocalWorkerCDK.java: Added a map as a input and output type
06:52 CIA-31 cdk: thomaskuhn * r9089 /trunk/cdk-taverna/src/main/java/org/openscienc​e/cdk/applications/taverna/io/FileReader.java: Removed an import
06:59 CIA-31 cdk: thomaskuhn * r9090 /trunk/cdk-taverna/src/main/java/org/open​science/cdk/applications/taverna/modeling​/Model3DBuildersWithMM2ForceField.java: Small changes, some Java 5 stuff...
06:59 CIA-31 cdk: thomaskuhn * r9091 /trunk/cdk-taverna/src/main/java/org/opens​cience/cdk/applications/taverna/modeling/M​odel3DBuildersWithMMFF94ForceField.java: Small changes, some Java 5 stuff...
07:00 CIA-31 cdk: thomaskuhn * r9092 /trunk/cdk-taverna/src/main/java/org/​openscience/cdk/applications/taverna/​qsar/AbstractAtomicDescriptor.java: Small changes, some Java 5 stuff...
07:01 CIA-31 cdk: thomaskuhn * r9093 /trunk/cdk-taverna/src/main/java/org/op​enscience/cdk/applications/taverna/qsar​/AbstractAtomicProtonDescriptor.java: Add this due to problems with proton descriptors
07:03 CIA-31 cdk: thomaskuhn * r9094 /trunk/cdk-taverna/src/main/java/org​/openscience/cdk/applications/tavern​a/qsar/AbstractBondDescriptor.java: Change the storage of the bond properties to the properties of the bonds. Was originally a property of the molecule, which cased problems
07:04 CIA-31 cdk: thomaskuhn * r9095 /trunk/cdk-taverna/src/main/java/org/openscience/c​dk/applications/taverna/qsar/QSARDescriptor.java: Small changes...
07:06 CIA-31 cdk: thomaskuhn * r9096 /trunk/cdk-taverna/src/main/java/org/openscience/​cdk/applications/taverna/qsar/descriptors/atomic/ (5 files): Changed the class which gets extended due to problems of the calculation of the RDF descriptors
07:08 CIA-31 cdk: thomaskuhn * r9097 /trunk/cdk-taverna/src/main/java/o​rg/openscience/cdk/applications/ta​verna/registry/QSARRegistry.java: Extend the QSAR registry to store the used UUID of the molecules for which qsar descriptors gets calculated
07:09 CIA-31 cdk: thomaskuhn * r9098 /trunk/cdk-taverna/src/main/java/o​rg/openscience/cdk/applications/ta​verna/smiles/SMILESGenerator.java: Small changes, some Java 5 stuff...
07:10 CIA-31 cdk: thomaskuhn * r9099 /trunk/cdk-taverna/src/main/java/org/openscience/​cdk/applications/taverna/tools/TagMolecules.java: Initial import of a worker which tags each molecule with a java UUID
07:11 CIA-31 cdk: thomaskuhn * r9100 /trunk/cdk-taverna/src/test/java/org/openscience/​cdk/applications/taverna/CDKTavernaTestData.java: Changed the smiles due to the change of the smiles parser within the cdk
07:13 CIA-31 cdk: thomaskuhn * r9101 /trunk/cdk-taverna/src/test/java/org/openscience​/cdk/applications/taverna/CDKTavernaTests.java: Remove this file because it is never used after the change to maven
07:15 CIA-31 cdk: thomaskuhn * r9102 /trunk/cdk-taverna/src/test/java/org/opens​cience/cdk/applications/taverna/modeling/M​odel3DBuildersWithMM2ForceFieldTest.java: Remove some old code and do some small changes and Java 5 stuff..
07:15 CIA-31 cdk: thomaskuhn * r9103 /trunk/cdk-taverna/src/test/java/org/opensc​ience/cdk/applications/taverna/modeling/Mod​el3DBuildersWithMMFF94ForceFieldTest.java: Remove some old code and do some small changes and Java 5 stuff..
07:16 CIA-31 cdk: thomaskuhn * r9104 /trunk/cdk-taverna/src/test/java/org/​openscience/cdk/applications/taverna/​qsar/AbstractDescriptorTestCase.java: Small changes, some Java 5 stuff...
07:17 CIA-31 cdk: thomaskuhn * r9105 /trunk/cdk-taverna/src/test/java/or​g/openscience/cdk/applications/tave​rna/qsar/QSARDescriptorTest.java: Small changes, some Java 5 stuff...
07:17 jonalv joined #cdk
07:18 CIA-31 cdk: thomaskuhn * r9106 /trunk/cdk-taverna/src/test/java/org/opensci​ence/cdk/applications/taverna/qsar/descripto​rs/atomic/InductiveAtomicSoftnessTest.java: Use wrong class within this test
07:57 CIA-31 cdk: thomaskuhn * r9107 /trunk/cdk-taverna/src/main/java/org/openscienc​e/cdk/applications/taverna/io/FileWriter.java: File writer to write txt and csv files this provides the possibility to save the vector with contains the calculated qsar values.
07:58 CIA-31 cdk: thomaskuhn * r9108 /trunk/cdk-taverna/src/main/java/org/openscience/​cdk/applications/taverna/io/WriteToCMLFile.java: Small changes, some Java 5 stuff...
07:58 CIA-31 cdk: thomaskuhn * r9109 /trunk/cdk-taverna/src/main/java/org​/openscience/cdk/applications/tavern​a/io/action/FileReaderAction.java: Changed comment
07:59 CIA-31 cdk: thomaskuhn * r9110 /trunk/cdk-taverna/src/main/java/org​/openscience/cdk/applications/tavern​a/io/action/FileWriterAction.java: File writer to write txt and csv files this provides the possibility to save the vector with contains the calculated qsar values. With a save file dialog.
07:59 CIA-31 cdk: thomaskuhn * r9111 /trunk/cdk-taverna/src/main/java/org/​openscience/cdk/applications/taverna/​io/action/ReadMDLMolFileAction.java: Changed comment
08:00 CIA-31 cdk: thomaskuhn * r9112 /trunk/cdk-taverna/src/main/java/org/o​penscience/cdk/applications/taverna/io​/action/ReadSMILESFromFileAction.java: Changed comment
08:01 CIA-31 cdk: thomaskuhn * r9113 /trunk/cdk-taverna/src/main/java/org/openscience/​cdk/applications/taverna/qsar/CSVGenerator.java: Worker which creates a list of string which has the format Comma separated value (CSV). The list contains the calculated qsar values.
08:04 CIA-31 cdk: thomaskuhn * r9114 /trunk/cdk-taverna/src/main/java/org/openscience/c​dk/applications/taverna/qsar/VectorGenerator.java: Worker which generate a vector of the molecule which stores calculated qsar values. This vector will be used later to generate the inputs for the data analysis steps
08:30 masak joined #cdk
09:01 jbrefort joined #cdk
10:36 rojasm left #cdk
10:37 rojasm joined #cdk
10:47 dleidert joined #cdk
11:06 egonw joined #cdk
11:23 thomas_ku joined #cdk
11:56 CIA-31 cdk: thomaskuhn * r9115 /trunk/cdk-taverna/src/main/java/org/open​science/cdk/applications/taverna/qsar/des​criptors/molecular/RuleOfFiveFilter.java: Small code changes and some Java 5 stuff..
11:56 CIA-31 cdk: thomaskuhn * r9116 /trunk/cdk-taverna/src/main​/resources/cdk.properties: Added the new worker to the config file
11:57 CIA-31 cdk: thomaskuhn * r9117 /trunk/cdk-taverna/src/main/resources​/META-INF/services/org.embl.ebi.escie​nce.scuflui.spi.ProcessorActionSPI: Added the new worker to the config file
11:57 CIA-31 cdk: thomaskuhn * r9118 /trunk/cdk-taverna/src/main/resources/META-​INF/services/org.openscience.cdk.applicatio​ns.taverna.scuflworkers.cdk.CDKLocalWorker: Added the new worker to the config file
11:58 CIA-31 cdk: thomaskuhn * r9119 /trunk/cdk-taverna/src/test/java/o​rg/openscience/cdk/applications/ta​verna/qsar/CSVGeneratorTest.java: Added a test case for the cvs generator
11:58 CIA-31 jmol: hansonr * r8439 /trunk/Jmol/src/org/jmol/ (8 files in 3 dirs): 11.3.33 PovRay output uses BufferedWriter
11:59 CIA-31 cdk: thomaskuhn * r9120 /trunk/cdk-taverna/src/test/java/or​g/openscience/cdk/applications/tave​rna/qsar/VectorGenerationTest.java: Add a test case for the vector generator
12:04 CIA-31 jmol: hansonr * r8440 /trunk/Jmol/src/org/jmol/ (2 files in 2 dirs): 11.3.33 Version # adds support for "xx'" atom designations in PDB and variable names
12:15 CIA-31 jmol: hansonr * r8441 /trunk/Jmol/src/org/jmol/viewer/ModelManager.java: 11.3.33 good to go
12:34 egonw grpmh... :(
12:34 egonw ethernet does not work on Linux on my new laptop :(
12:35 thomas_ku joined #cdk
12:37 CIA-31 cdk: thomaskuhn * r9121 /trunk/cdk-taverna/src/test/java/org/openscience​/cdk/applications/taverna/CMLChemfileTest.java: Added a test for testing the to cml method of the cmlchemfile object
12:37 rojasm I have the same problem
12:37 rojasm :(
12:37 egonw what laptop do you have?
12:37 rojasm acer
12:37 egonw I got a brand new HP 6720s
12:38 rojasm ooooo
12:38 egonw intel chipset
12:38 CIA-31 cdk: thomaskuhn * r9122 /trunk/cdk-taverna/src/test/java/org/open​science/cdk/applications/taverna/qsar/des​criptors/molecular/RuleOfFiveTest.java: Small code changes and some Java 5 stuff..
12:38 egonw 82562GT
12:39 rojasm exactly the network works but not the wireless
12:39 rojasm but that is with the new Ubuntu 7.10
12:39 CIA-31 cdk: thomaskuhn * r9123 /trunk/cdk-taverna/src/test/java/org​/openscience/cdk/applications/tavern​a/smiles/SMILESGeneratorTest.java: Small code changes and some Java 5 stuff..
12:39 egonw ah... OK, have not tested WLAN yet...
12:39 egonw but my ethernet is not working
12:39 rojasm achso
12:40 egonw and since we have no WLAN here... I'm pretty pissed...
12:40 egonw also because the ICT department found it necessary to delete the Vista in favor of the XP...
12:40 rojasm I don't have as well. But I build one for me :)
12:40 egonw but *failed* with XP install...
12:40 egonw lack of drivers...
12:40 egonw so, got a pretty broken machine now :(
12:40 CIA-31 cdk: thomaskuhn * r9124 /trunk/cdk-taverna/src/test/java/o​rg/openscience/cdk/applications/ta​verna/tools/TagMoleculesTest.java: Added a test for the tag molecule worker
12:40 egonw thomas_ku: what's that doing?
12:40 egonw uploading tags to Connotea?
12:41 rojasm a lot of updates
12:41 thomas_ku no this is only the test for a woker which gives molecules a java UUID
12:41 egonw ah, good :)
12:42 * egonw is very much looking forward to documentation on your architecture :)
12:42 thomas_ku this id will be used to find the molecules after you create a vector for a qsar analysis which only get the vector not the whole molecule
12:44 thomas_ku but will need some more time for a good documentation and for example workflow... etc
12:47 egonw but that sounds very good...
12:48 thomas_ku we will see...
12:48 egonw that is actually one of the questions we had...
12:48 egonw how to keep track of object IDs...
12:49 CIA-31 cdk: thomaskuhn * r9125 /trunk/cdk-taverna/pom.xml: Small config changes
12:50 thomas_ku yeah I do this only internally currently and than save the mole as cml with all calculated properties and the molecule ID so that you can find it at least
12:51 thomas_ku It is not the best solution but I think it is a beginning to store your results
12:52 carsten joined #cdk
12:56 CIA-31 cdk: thomaskuhn * r9126 /trunk/cdk-taverna/src/main/java/org/op​enscience/cdk/applications/taverna/qsar​/DescriptorCalculatorLocalWorker.java: Comment out this class due to the new general qsar worker...
12:57 CIA-31 cdk: thomaskuhn * r9127 /trunk/cdk-taverna/src/test/java/org/ope​nscience/cdk/applications/taverna/qsar/D​escriptorCalculatorLocalWorkerTest.java: Comment out this class due to the new general qsar worker...
13:33 jpansanel moin
13:34 egonw hi jpansanel
13:37 egonw jpansanel: how well does mychem scale?
13:37 egonw that is, can it handle 20M compounds? say the ChemSpider content?
13:37 jpansanel I don't known
13:38 jpansanel I didn't Mychem on a big database
13:38 jpansanel I've some issues because OpenBabel is not thread safe
13:42 egonw ah, ic
13:48 CIA-31 jmol: hansonr * r8442 /trunk/Jmol/src/org/jmol/ (8 files in 4 dirs): 11.3.33 Povray light tweak good to go
13:49 CIA-31 bioclipse: carl_masak * r3981 /trunk/plugins/net.bioclipse.rhino/src/net/bi​oclipse/plugins/bc_rhino/ScriptingTools.java:
13:49 CIA-31 bioclipse: [ScriptingTools.java]
13:49 CIA-31 bioclipse: * typo hunt
13:49 CIA-31 bioclipse: * if statement -> ?:
13:52 jpansanel joined #cdk
14:33 * egonw has gone home
14:56 CIA-31 bioclipse: ospjuth * r3982 /trunk/playground/plugins/net.bio​clipse.biomoby/src/net/bioclipse/ (4 files in 3 dirs): Complete rewrite of BioMoby GUI generation up to Primary Inputs.
15:10 CIA-31 jmol: hansonr * r8443 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs): 11.3.33/11.3.34 better geoSurface rendering
15:38 CIA-31 jmol: hansonr * r8444 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs): code tweak.
17:49 egonw joined #cdk
18:30 CIA-31 jmol: hansonr * r8445 /trunk/Jmol/src/org/jmol/viewer/ (Compiler.java Jmol.properties): 11.3.33/11.3.34 bug fix: select [set] or [2mo] or [db']
18:35 CIA-31 jmol: nicove * r8446 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
18:44 CIA-31 jmol: hansonr * r8447 /trunk/Jmol/src/org/jmol/viewer/Viewer.java: 11.3.33/11.3.34 bug fix: -c flag errors not going to Logger.Error
18:47 CIA-31 jmol: hansonr * r8448 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.34 bug fix: -c flag errors not going to Logger.Error
19:34 CIA-31 bioclipse: shk3 * r3983 /trunk/plugins/net.bioclipse.spectrum/ (doc/charts.html src/spok/gui/SpectrumChartFactory.java): started hightlighting in peak view
20:05 CIA-31 cdk: egonw * r9128 /trunk/cdk/src/org/openscience/cdk/aromat​icity/CDKHueckelAromaticityDetector.java: Added a new Hueckel-based aromaticity detector, using the new atom types
20:59 CIA-31 jmol: hansonr * r8449 /trunk/Jmol/src/org/jmol/adapter​/readers/cifpdb/CifReader.java: 11.3.34 optional _site field in CIF files
21:00 CIA-31 bioclipse: egonw * r3984 /trunk/plugins/net.bioclipse.cdk.descriptor/src/ne​t/bioclipse/extensions/CDKDescriptorProvider.java: Return all vector values
21:27 CIA-31 bioclipse: shk3 * r3985 /trunk/plugins/net.bioclipse.spectrum/src/ (2 files in 2 dirs): avoids npes

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