Camelia, the Perl 6 bug

IRC log for #cdk, 2008-01-24

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All times shown according to UTC.

Time Nick Message
03:34 CIA-18 cdk: rajarshi * r9949 /trunk/cdk/src/org/openscience/​cdk/qsar/descriptors/molecular/ (BCUTDescriptor.java WHIMDescriptor.java): Cleaned up WHIM code a bit and fixed BCUT code so that it actually uses the cloned input molecule
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08:34 CIA-18 bioclipse: ospjuth * r4793 /branches/bioclipse2/bioinformatics​/plugins/net.bioclipse.biojava.ui/ (2 files in 2 dirs): Added dummy action for Proteins.
08:34 CIA-18 bioclipse: ospjuth * r4794 /branches/bioclipse2/bioinformatics/​plugins/net.bioclipse.biojava.ui.tes​t/src/net/bioclipse/biojava/ui/test/ (6 files in 2 dirs): Added more test for SequenceContentProvider.
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08:52 egonw moin
08:52 rojasm moin egonw
08:52 egonw hi rojasm
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11:12 thomas_ku moin
11:12 thomas_ku egonw: around?
11:15 egonw yes
11:16 thomas_ku a short question
11:16 thomas_ku do the smiles generator creates aromatic simles in a fashion like c1ccccc1 with the small c?
11:17 egonw not by default...
11:18 egonw as the reader could not handle it well enough
11:18 egonw so, it will output the kekule form passed as input
11:19 thomas_ku ok i I have an aromatic ring within the cdk and will create the smiles from it it will not give me the c1ccccc1
11:19 thomas_ku right?
11:19 egonw no, it will give you C1=CC=CC=C1
11:20 thomas_ku So the cdk is currently not able to create the aromatic smiles!
11:20 egonw I think there is an option to do that
11:21 thomas_ku Ok any idea what its name was
11:22 egonw http://cheminfo.informatics.indiana.edu​/~rguha/code/java/nightly/api/org/opens​cience/cdk/smiles/SmilesGenerator.html
11:22 egonw setUseAromaticityFlag()
11:22 thomas_ku Ok just saw it too
11:22 thomas_ku thanks
11:23 thomas_ku I will test it
12:42 CIA-18 bioclipse: carl_masak * r4795 /branches/bioclipse2/core/plugins/net.biocl​ipse.recording/src/net/bioclipse/recording/ (JSScriptGenerator.java JsScriptGenerator.java):
12:42 CIA-18 bioclipse: [JSScriptGenerator -> JsScriptGenerator]
12:42 CIA-18 bioclipse: * Easier to read
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13:33 CIA-18 bioclipse: carl_masak * r4796 /branches/bioclipse2/core/plugins/net.bi​oclipse.recording.tests/src/net/bioclips​e/recording/ScriptGenerationTests.java:
13:33 CIA-18 bioclipse: [ScriptGenerationTests.java]
13:33 CIA-18 bioclipse: * chased earlier name change
13:34 CIA-18 bioclipse: carl_masak * r4797 /branches/bioclipse2/core/plugins/​net.bioclipse.ui/src/net/bioclipse​/ui/views/ActionHistoryView.java:
13:34 CIA-18 bioclipse: [ActionHistoryView.java]
13:34 CIA-18 bioclipse: * chased earlier name change
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13:36 CIA-18 bioclipse: carl_masak * r4798 /branches/bioclipse2/ (5 files in 5 dirs):
13:36 CIA-18 bioclipse: [net.bioclipse.core]
13:36 CIA-18 bioclipse: [net.bioclipse.recording]
13:36 CIA-18 bioclipse: [net.bioclipse.biojava.business]
13:36 CIA-18 bioclipse: [net.bioclipse.springBasedPrototypePlugin]
13:36 CIA-18 bioclipse: * methods are subject to recording according to whitelisting
13:36 CIA-18 bioclipse:  (with the annotation @Recorded) instead of blacklisting
13:37 CIA-18 bioclipse: jonalv * r4799 /branches/bioclipse2/core/plugins/ (2 files in 2 dirs): No need to implicitly start recording plugin now since the plugin is started when one of it's class files is loaded
14:18 CIA-18 bioclipse: carl_masak * r4800 /branches/bioclipse2/core/plugins/n​et.bioclipse.ui/src/net/bioclipse/u​i/views/ScriptingConsoleView.java:
14:18 CIA-18 bioclipse: [ScriptingConsoleView.java]
14:18 CIA-18 bioclipse: * Bound SWT.ARROW_RIGHT to a more sensible action
15:08 CIA-18 bioclipse: ospjuth * r4801 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (10 files in 5 dirs): Added an extension point for installing data folders in the NewSampleDataProjectWizard. Wizard now operational.
15:13 CIA-18 bioclipse: ospjuth * r4802 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (data/AminoAcids/ data/amino_acids/ plugin.xml): Renamed to AminoAcids
15:16 CIA-18 bioclipse: ospjuth * r4803 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (data/Qresources/ data/ScriptingResources/ plugin.xml): Updated sample data folders and implemented EP.
15:23 CIA-18 bioclipse: ospjuth * r4804 /branches/bioclipse2/misc/ne​t.bioclipse.data.sampledata/ (2 files in 2 dirs): Updated EP implementation. This plugin now works.
16:26 CIA-18 bioclipse: Annzi * r4805 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/: Initial import.
16:27 CIA-18 bioclipse: Annzi * r4806 /branches/bioclipse2/chemoinf​ormatics/net.bioclipse.moss/ (59 files in 8 dirs): Initial import.
17:22 Annzi left #cdk
17:26 CIA-18 bioclipse: jonalv * r4807 /branches/bioclipse2/ (22 files in 9 dirs): Merged net.bioclipse.recording into net.bioclipse.core
17:27 CIA-18 bioclipse: jonalv * r4808 /branches/bioclipse2/core/plug​ins/net.bioclipse.recording/: removed net.bioclipse.recording
17:27 CIA-18 bioclipse: carl_masak * r4809 /branches/bioclipse2/core/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/views/JsConsoleView.java:
17:27 CIA-18 bioclipse: [JsConsoleView.java]
17:27 CIA-18 bioclipse: * Console now complains if R is not installed
17:35 CIA-18 bioclipse: jonalv * r4810 /branches/bioclipse2/core/plug​ins/net.bioclipse.core.tests/ (12 files in 9 dirs): moved recording tests into net.bioclipse.core.tests
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