Camelia, the Perl 6 bug

IRC log for #cdk, 2007-12-19

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All times shown according to UTC.

Time Nick Message
01:36 CIA-17 jmol: hansonr * r8812 /trunk/Jmol/src/org/jmol/ (5 files in 3 dirs): (log message trimmed)
01:36 CIA-17 jmol: version=11.3.61
01:36 CIA-17 jmol: # bug fix: draw not colored
01:36 CIA-17 jmol: # bug fix: mousewheel too low power
01:36 CIA-17 jmol: # bug fix: select */4 when "4" is inappropriate returns all instead of none
01:36 CIA-17 jmol: # bug fix: memory leak in applet due to mouse/hoverwatcher listeners
01:36 CIA-17 jmol: # bug fix: applets not self-destroying when window containing them close
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02:44 CIA-17 jmol: hansonr * r8813 /trunk/Jmol/src/org/jmol/ (3 files in 2 dirs): version=11.3.61 # bug fix: select 1.5 in trajectory context should switch to that set of coordinates
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09:33 jpansanel moin
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11:22 CIA-17 bioclipse: egonw * r4550 /trunk/plugins/net.bioclipse.joelib/ (doc/ doc/cdk_home.html doc/joelib.html toc.xml): Added info about JOElib to the help
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11:33 CIA-17 bioclipse: egonw * r4551 /trunk/plugins/net.bioclipse.joelib/plugin.xml: Installed the help
11:33 CIA-17 bioclipse: egonw * r4552 /trunk/plugins/net.bioclipse.statistics/sr​c/net/bioclipse/model/MatrixResource.java: Added the missing setRowName()
11:33 CIA-17 bioclipse: biocoder * r4553 /trunk/plugins/net.bioclipse.statistics/src/​net/bioclipse/editors/MatrixGridEditor.java: When choosing only 2 columns no dialog is shown
11:35 CIA-17 bioclipse: egonw * r4554 /trunk/plugins/net.bioclipse.descriptor/src/net​/bioclipse/jobs/DescriptorCalculationJob.java: Set row name after file name
11:54 CIA-17 bioclipse: egonw * r4555 /trunk/plugins/net.bioclipse.statistics/src/net/bi​oclipse/model/IMatrixImplementationResource.java: Added label support to the interface
12:46 rojas1 hi all question: how to present the elemental composition from a mas with an element which two different isotopes for example C(12,13). e.g. C3C1H5 or C(^12)3C(^13)1H5 or just C4H5
12:46 rojas1 Because I can not find some reference in google
12:47 rojas1 how to write it
12:52 egonw not sure...
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13:15 CIA-17 bioclipse: egonw * r4556 /trunk/plugins/ (5 files in 4 dirs): Added file name as row labels
13:18 CIA-17 cdk: miguelrojasch * r9635 /branches/miguelrojasch/mf​/src/org/openscience/cdk/ (2 files in 2 dirs): unlimited isotopes for calculating the elemental composition formula; Access to obtain elemental composition with different isotopes from the same element e.g. C(^12)3C(^13)H6
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13:39 CIA-17 jmol: hansonr * r8814 /trunk/Jmol/src/org/jmol/shapespecial/Dipole.java: temp
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13:45 CIA-17 jmol: hansonr * r8815 /trunk/Jmol/src/org/jmol/ (14 files in 5 dirs): version=11.3.61 # code: dipoles moved to shapespecial
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14:31 CIA-17 jmol: hansonr * r8816 /trunk/Jmol/src/org/jmol/ (15 files in 6 dirs): code refactoring
14:34 CIA-17 jmol: hansonr * r8817 /trunk/Jmol/src/org/jmol/mo​delsetbio/Quaternion.java:
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14:36 CIA-17 jmol: hansonr * r8818 /trunk/Jmol/src/org/jmol/modelsetbio/ (AminoMonomer.java Monomer.java NucleicMonomer.java): code refactoring
14:47 CIA-17 jmol: hansonr * r8819 /trunk/Jmol/src/org/jmol/mod​elset/ModelCollection.java: version=11.3.61 # bug fix: quaternions broken in 11.3.58
14:47 CIA-17 jmol: hansonr * r8820 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: version=11.3.61 # bug fix: quaternions broken in 11.3.58
15:15 egonw olas, steinbeck, rojas1: http://chem-bla-ics.blogspot.com/2007/1​2/test-results-for-cdk-10x-branch.html
15:15 egonw obligatory reading
15:16 steinbeck yes, Sir!
15:17 egonw btw, the required computation time:
15:17 egonw 214437 2007-12-17 17:15 ant_r8350.log
15:17 egonw 20222 2007-12-19 00:47 ant_r9403.log
15:17 egonw so, about 29.5 hours :)
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15:25 CIA-17 jmol: hansonr * r8821 /trunk/Jmol/src/org/jmol/viewer/ (Jmol.properties StateManager.java): version=11.3.61 # bug fix: dipoleScale not saved in state
15:25 CIA-17 bioclipse: ospjuth * r4557 /trunk/playground/plugins/net.bioclipse.biomoby/ (51 files in 4 dirs): Updated to BioMoby as of 2007-12-19.
15:30 CIA-17 bioclipse: ospjuth * r4558 /trunk/playground/plugins/net.bioclipse.biomoby/ (47 files in 2 dirs): Updated to BioMoby as of 2007-12-19.
15:31 CIA-17 bioclipse: ospjuth * r4559 /trunk/playground/plugins/net.bioclipse.​biomoby.ui/src/net/bioclipse/biomoby/ui/ (7 files in 5 dirs): A lot of updates to Biomoby UI. Trying to reach a state where simple functionality works. Now it is very unstable.
15:36 CIA-17 jmol: hansonr * r8822 /trunk/Jmol/src/org/jmol/shape​special/DipolesRenderer.java: 11.3.61 -- final change -- dipole rendering tweak
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15:43 CIA-17 bioclipse: egonw * r4560 /trunk/plugins/net.bioclipse.descriptor/src/net​/bioclipse/jobs/DescriptorCalculationJob.java: Don't overwrite, but pick a new name
15:47 CIA-17 bioclipse: ospjuth * r4561 /trunk/playground/plugins/net.bioclips​e.biomoby.ui/src/net/bioclipse/biomoby​/ui/scripts/MobyServiceScripting.java: IScriptProvider -> INameSpaceProvider
15:50 CIA-17 bioclipse: egonw * r4562 /trunk/plugins/ (2 files in 2 dirs): Support an extra result type
15:56 CIA-17 bioclipse: egonw * r4563 /trunk/plugins/net.bioclipse.joelib.​descriptor/src/net/bioclipse/extensi​ons/JOELibDescriptorProvider.java: Only do the easy descriptors (not those with matrix results)
16:04 CIA-17 bioclipse: egonw * r4564 /trunk/plugins/net.bioclipse.cdk.descriptor/src/ne​t/bioclipse/extensions/CDKDescriptorProvider.java: The IP descriptor is not stable
16:06 CIA-17 bioclipse: ospjuth * r4565 /trunk/playground/plugins/net.bioclipse.​biomoby.ui/src/net/bioclipse/biomoby/ui/ (BioMobyConstants.java prefs/RegistriesPreferencePage.java): Updated to new moby server endpoint.
16:46 CIA-17 jmol: hansonr * r8823 /trunk/Jmol/src/org/jmol/ (shapebio/BioShapeCollection.java viewer/Jmol.properties): version=11.3.61 # bug fix: multifile cartoons improperly rendering in all frames
16:53 CIA-17 bioclipse: egonw * r4566 /trunk/plugins/ (2 files in 2 dirs): Some warnings: trying to figure out where those NULLs come from
16:54 CIA-17 bioclipse: egonw * r4567 /trunk/plugins/net.bioclipse.statistics.jam​a/src/net/bioclipse/model/JamaMatrix.java: Fixed a NPE
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20:22 CIA-17 cdk: egonw * r9636 /trunk/cdk/src/org/openscience/cdk/qs​ar/descriptors/molecular/ALOGP.java: Full imports, cleaned up JavaDoc (removed newline)
20:29 CIA-17 cdk: egonw * r9637 /trunk/cdk/src/org/openscience/cdk​/test/qsar/descriptors/molecular/ (44 files): More testing of the IMolecularDescriptor's: verify that the column labels are available, and as many as calculated descriptor values
20:45 CIA-17 jmol: nicove * r8824 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
20:47 olas left #cdk
21:18 CIA-17 cdk: egonw * r9638 /trunk/cdk/src/ (18 files in 5 dirs): Setting up coverage testing for the molecular descriptors
22:32 CIA-17 jmol: hansonr * r8825 /trunk/Jmol/src/org/jmol/ (12 files in 5 dirs):
22:32 CIA-17 jmol: version=11.3.62_dev PDB structure update
22:32 CIA-17 jmol: # bug fix: Jmol not putting structures in for all models in a PDB file
22:32 CIA-17 jmol: # bug fix: calculate polymers (never documented) not necessary -- calculate structure suffices
22:32 CIA-17 jmol: # bug fix: calculate structure updated for ignoring jmolDataFrames and using currently selected atoms
23:04 CIA-17 jmol: hansonr * r8826 /trunk/Jmol/src/org/jmol/ (modelset/ModelSet.java viewer/Eval.java):
23:05 CIA-17 jmol: hansonr * r8827 /trunk/Jmol/src/org/jmol/viewer/Eval.java:

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