Camelia, the Perl 6 bug

IRC log for #cdk, 2008-05-23

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All times shown according to UTC.

Time Nick Message
00:21 CIA-31 jmol: hansonr * r9409 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): (log message trimmed)
00:21 CIA-31 jmol: version=11.5.38 cross(a,b) and bug fix for draw scale in multiple model
00:21 CIA-31 jmol: # bug fix: scaling of draw object for multimodel environment can cause null pointer exception
00:21 CIA-31 jmol: # bug fix: scaling of VECTOR was from center, not origin
00:21 CIA-31 jmol: # bug fix: select n-m:c chain selection inappropriately case sensitive
00:21 CIA-31 jmol: # bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way
00:21 CIA-31 jmol: # bug fix: draw CIRCLE for multiple models
03:06 CIA-31 jmol: hansonr * r9410 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): version=11.5.38 sin(x) cos(x)
03:13 CIA-31 jmol: hansonr * r9411 /trunk/Jmol/src/org/jmol/m​odelset/Measurement.java: version=11.5.38 # bug fix: pm rounding to integer value
03:15 CIA-31 jmol: hansonr * r9412 /branches/v11_4/Jmol/src/org/​jmol/viewer/Jmol.properties: 11.4.4 # bug fix: pm rounding to integer value
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06:27 thomas_ku moin
06:27 CIA-31 bioclipse: ospjuth * r5685 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.ui/ (18 files in 9 dirs): Provides molecule content via CDK10 and makes SDFiles expandabe in Navigator.
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08:38 CIA-31 bioclipse: ospjuth * r5686 /bioclipse2/trunk/plugins/ne​t.bioclipse.cdk10.sdfeditor/ (6 files in 3 dirs): Added a content outline for SDFiles. If clicked in outline, selects corresponding row in structureTable.
08:51 CIA-31 bioclipse: ospjuth * r5687 /bioclipse2/trunk/plugins/net.bioclipse.cdk10​.sdfeditor/src/net/bioclipse/cdk10/sdfeditor/ (editor/StructureTablePage.java outline/SDFOutlinePage.java): Changes in selections in StructureTable and Outline are now synchronized.
09:18 CIA-31 bioclipse: ospjuth * r5688 /bioclipse2/trunk/plugins/ (5 files in 2 dirs): Synchronized JCPPage with selections in outline, table, and toolbar.
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09:29 CIA-31 bioclipse: ospjuth * r5689 /bioclipse2/trunk/plugins/net.bioclips​e.cdk10.sdfeditor/src/net/bioclipse/cd​k10/sdfeditor/editor/SDFJCPPage.java: Removed debug line.
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09:59 CIA-31 cdk: miguelrojasch * r11127 /cdk/branches/miguelrojasch-IP/.classpath: removed java imports in .classpath
10:03 CIA-31 cdk: miguelrojasch * r11128 /cdk/branches/miguelrojasch-IP/src/test/org/ope​nscience/cdk/tools/HOSECodeGeneratorTest.java: reversed to previous commit without comments. My fail
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11:39 CIA-31 bioclipse: ospjuth * r5690 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.sdf​editor/src/net/bioclipse/cdk10/sdfeditor/editor/ (3 files): It is now possible to edit indivudual properties in the SDFileEditor. doSave() and doSaveAs() are not yet implemented.
11:40 CIA-31 jmol: hansonr * r9413 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: rounding
11:42 CIA-31 jmol: hansonr * r9414 /branches/v11_4/Jmol/src/org/j​mol/modelset/Measurement.java: 11.4.4 # bug fix: pm rounding to integer value
11:56 CIA-31 cdk: archvile18 * r11129 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java:
11:56 CIA-31 cdk: Modified isAcceptable() to verify atom types. Fixes 4 of 5 failing
11:56 CIA-31 cdk: DeduceBondSystemToolTest cases. Closes bug #1969642. The remaining failing test
11:56 CIA-31 cdk: is submitted as bug #1970365. Two CDKAtomTypeMatcherTest cases now fail.
11:56 CIA-31 cdk: Submitted as #1970371.
12:02 CIA-31 cdk: archvile18 * r11130 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Fixes bug #1969854 "Quinone oxygens incorrectly typed O.planar3".
12:20 CIA-31 jmol: hansonr * r9415 /trunk/Jmol/src/org/jmol/viewer/Eval.java:
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12:48 Andreas1 Hi egonw
12:48 egonw hi
12:50 Andreas1 Atom typing is like a cat biting its own tail...
12:50 egonw yeah, if every one would just use explicit information...
12:51 egonw I mean, I'm understand not being able to work out stuff if info is missing... e.g. hydrogen locations in x-ray data...
12:51 egonw but having so much trouble because people do no use explicit hydrogens and/or bond orders, is just bloody anoying...
12:52 Andreas1 ...but implicity is just so convenient...
12:52 egonw for writing, sure...
12:52 egonw for reading ... then you pay
12:52 Andreas1 so true
12:53 egonw got to go again... pick up son from school
12:53 egonw bye again
12:53 Andreas1 I'll commit a little add-on to the isAcceptable()-checks
12:53 Andreas1 cu later
13:02 CIA-31 cdk: archvile18 * r11131 /cdk/trunk/src/main/org/openscience/c​dk/atomtype/CDKAtomTypeMatcher.java: Extended isAcceptable() to check container.getBondOrderSum(atom) against type.getValency().
13:13 CIA-31 jmol: hansonr * r9416 /trunk/Jmol/src/org/jmol/ (g3d/Sphere3D.java shapespecial/EllipsoidsRenderer.java): version=11.5.38 # bug fix: thermal ellipsoids for improper values
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13:50 CIA-31 bioclipse: egonw * r5691 /bioclipse2/trunk/plugins/net.bioclipse​.cdk10.jchempaint/src/net/bioclipse/cdk​10/jchempaint/ui/editor/JCPPage.java: Don't silently eat exceptions
14:03 CIA-31 bioclipse: ospjuth * r5692 /bioclipse2/trunk/plugins/net.bioclipse.cdk10​.sdfeditor/src/net/bioclipse/cdk10/sdfeditor/ (CDK10Manager.java editor/SDFEditor.java): Implemented doSave(). CDK's MDLEditor doesn't save properties automatically, FIXME placed in CDK10Manager for egonw.
14:09 CIA-31 cdk: miguelrojasch * r11132 /cdk/branches/miguelrojasch-IP/src/ (2 files in 2 dirs): Changed the model function for Halogen. Root mean squared error 0.5817.
14:28 CIA-31 cdk: egonw * r11133 /cdk/trunk/META-INF/MANIFEST.MF: Some tweaks, to get Bioclipse2 use this plugin directly
14:30 CIA-31 bioclipse: egonw * r5693 /bioclipse2/trunk/plugins/net.bioclipse.cdk10.s​dfeditor/src/net/bioclipse/cdk10/sdfeditor/io/ (. SDFWriter.java): Added a SD file writer that outputs all IMolecule.getProperties()
14:30 CIA-31 bioclipse: egonw * r5694 /bioclipse2/trunk/plugins/ (6 files in 6 dirs): Use org.openscience.cdk from CDK SVN directly, instead of the net.bioclipse.cdk wrapper with svn:externals
14:57 CIA-31 bioclipse: goglepox * r5695 /bioclipse2/trunk/plugins/net.bioclipse.services/ (8 files in 4 dirs): Added functionality for updating the tree view when new services is added.
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16:04 Topic for #cdkis now The Chemistry Development Kit (http://cdk.sf.net) | JUnit: 6043, 64 fails + 59 errors (2.04%) | 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: http://www.cdknews.org/
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