Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-24

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All times shown according to UTC.

Time Nick Message
01:02 CIA-15 jmol: hansonr * r8501 /trunk/Jmol/src/org/jmol/ (4 files in 2 dirs): version=11.3.37_dev # bug fix: -- adds antialiasing for translucent objects
02:14 CIA-15 jmol: hansonr * r8502 /trunk/Jmol/src/org/ (3 files in 2 dirs): version=11.3.37_dev # bug fix: POV-Ray dialog upgrade
02:38 CIA-15 jmol: hansonr * r8503 /trunk/Jmol/src/org/jmol/ (g3d/Graphics3D.java viewer/Viewer.java): version=11.3.37_dev # bug fix: antialias upgrade
02:45 CIA-15 jmol: hansonr * r8504 /trunk/Jmol/src/org/jmol/export/_Exporter.java: version=11.3.37_dev # bug fix: POV-Ray file writing fix?
02:48 CIA-15 jmol: hansonr * r8505 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: (log message trimmed)
02:48 CIA-15 jmol: 11.3.37 VERSION
02:48 CIA-15 jmol: # new feature: @{mathExpression} for echos, select, etc. where @x can be used.
02:48 CIA-15 jmol: # select atomno=@{x*2}
02:48 CIA-15 jmol: # color atoms @{xlist[n]}
02:48 CIA-15 jmol: # new feature: {atomExpression}.color = "red" (or "[xff0000]" or {255,0,0}
02:48 CIA-15 jmol: # new feature: helixes as barrels in cartoons or rockets using
02:49 CIA-15 jmol: hansonr * r8506 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties:
02:49 CIA-15 jmol: hansonr * r8507 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties:
02:53 CIA-15 jmol: hansonr * r8508 /trunk/Jmol/src/org/jmol/viewer/Viewer.java: 11.3.37 (resizeImage fix)
05:48 CIA-15 jmol: nicove * r8509 /trunk/Jmol/src/org/jmol/translation/Jmol/ (11 files): Update of .po files
05:49 rojasm joined #cdk
05:58 CIA-15 jmol: nicove * r8510 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: Version
07:49 jonalv joined #cdk
08:42 masak joined #cdk
09:16 jpansanel moin
09:16 masak moin jpansanel
09:16 jpansanel hi masak
09:18 egonw joined #cdk
09:21 masak egonw: just checking: should things in n.b.plugins.views really be in n.b.views nowadays?
09:23 egonw ummm... don't remember... there should be something in the wiki about that...
09:23 egonw mom
09:23 masak not extremely important, I'm just curious
09:23 egonw http://wiki.bioclipse.net/inde​x.php?title=Coding_Conventions
09:24 egonw OK, no conventions on package names yet...
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13:02 CIA-15 jmol: hansonr * r8511 /trunk/Jmol/src/org/jmol/ (3 files in 3 dirs): version=11.3.38_dev # bug fix: POV-Ray file writing fix?
13:17 CIA-15 jmol: hansonr * r8512 /trunk/Jmol/src/org/jmol/shape/FrankRenderer.java:
13:30 CIA-15 cdk: egonw * r9187 /trunk/cdk/src/org/openscience/cdk/test​/atomtype/CDKAtomTypeMatcherTest.java: Placed in correct module; fixed JavaDoc
13:31 CIA-15 cdk: egonw * r9188 /trunk/cdk/src/org/openscienc​e/cdk/test/CDKTestCase.java: Complain if atom type is not perceived
13:41 masak joined #cdk
13:56 masak egonw: how would I do if I wanted a thorough understanding of the class hierarchy in the vicinity of AtomContainer in cdk?
13:57 masak we're thinking of Bioclipse2 design right now, and a lot of these things are coming up
13:57 egonw masak: mom...
13:57 masak no hurry
13:57 egonw http://chem-bla-ics.blogspot.co​m/2007/07/cdk-data-model-1.html
13:57 egonw have not come around to #2 etc...
13:57 egonw it's on my list...
13:58 egonw if you have specific questions... please add a comment to that blog item
13:58 masak I will
13:58 masak thx
14:01 CIA-15 cdk: egonw * r9189 /trunk/cdk/src/org/openscience/cdk/test​/atomtype/CDKAtomTypeMatcherTest.java: Added propyne as test.
14:01 masak I have one specific question already
14:01 egonw go ahead
14:01 masak olas mentioned that you dislike the name "Molecule" in the data model
14:01 masak tending towards names like "atom container"
14:02 masak I think I see the rationale for that, just want to make sure I got it right
14:02 egonw depends on how used...
14:02 masak "Molecule" is often a too narrow term, yes?
14:02 egonw a molecule is one fully connected structure
14:02 masak ok
14:02 egonw a salt is not a molecule, per this definatino
14:02 jbrefort joined #cdk
14:02 masak no
14:03 masak OTOH, it's not very often that I open a salt in an editor in order to visualize it and operate on it
14:07 egonw well... quite common in pharma...
14:07 CIA-15 bioclipse: ospjuth * r4043 /trunk/playground/plugins/net.bioclip​se.biomoby/src/net/bioclipse/biomoby/ (3 files in 2 dirs): Better handling of results in MobyObjectBytes and MobyObjectString. Still not perfect though.
14:07 egonw where most drugs are actually salts in the pills
14:07 masak egonw: I guess my question is, is there a compelling reason not to name our Molecule interdace "IMolecule"?
14:08 masak s/interdace/interface/
14:09 egonw not other than semantics...
14:10 masak well, "Molecule" feels like it conjures up better images than "AtomContainer"
14:10 masak but I wouldn't want us to use it if, say, 50% of the Molecules we had weren't really molecules
14:19 egonw I would be fine with the use of 'molecule' in BC2 scripting
14:21 masak good
14:21 masak our two chief examples right now are Molecule and Sequence
14:21 masak we figure we'll set up a prototype where one can play around with those
14:22 masak just to get a feel for the API and what is needed
14:30 egonw ack, sounds good
14:36 CIA-15 cdk: rajarshi * r9190 /trunk/cdk/tools/nightly.py: Updated nightly to correctly parse Junit test output
14:37 CIA-15 cdk: rajarshi * r9191 /trunk/cdk/tools/nightly.py: Got rid of some debugging code
14:38 CIA-15 cdk: egonw * r9192 /trunk/cdk/src/org/openscience/cdk/test/atomt​ype/CDKAtomTypeMatcherTestFileReposTest.java: Don't count neighbors for the 'X' atom type
14:39 CIA-15 cdk: egonw * r9193 /trunk/cdk/src/org/openscience/cdk/ (3 files in 3 dirs): Fixed mistyping: S.2 != S.planar3
14:41 CIA-15 cdk: egonw * r9194 /trunk/cdk/src/org/openscience/cdk​/test/qsar/descriptors/atomic/Atom​HybridizationDescriptorTest.java: Cleaned up code: just throw exception, use CDKTestCase.addImplicitHydrogens(), just throw Exception
15:00 CIA-15 cdk: egonw * r9195 /trunk/cdk/src/org/openscience/cdk/ (2 files in 2 dirs): Fixed detection of phosphine species, such as the added diethyl phosphine
15:15 CIA-15 cdk: egonw * r9196 /trunk/cdk/src/org/openscience/cdk/test/qsar/d​escriptors/atomic/IPAtomicDescriptorTest.java: Added some extra assertions: the problem is the creation of the reaction.
15:16 CIA-15 cdk: egonw * r9197 /trunk/cdk/src/org/opensci​ence/cdk/qsar/descriptors/ (3 files in 2 dirs): Fixed three more IAtom not found in cloned AtomContainer twin
15:18 CIA-15 bioclipse: jonalv * r4044 /trunk/playground/plugins/​net.bioclipse.structuredb/ (8 files in 4 dirs): Created business object StructuredbManager but ran into trouble with managing multiple datasources. Waiting for feedback from Spring forum now...
15:19 CIA-15 bioclipse: ospjuth * r4045 /trunk/playground/plugins/net.bioclipse.biomoby/ (META-INF/MANIFEST.MF about.ini build.properties): Updated build for inclusion in a feature
16:07 CIA-15 bioclipse: carl_masak * r4046 /net.bioclipse.case-feature/: net.bioclipse.case-feature does not belong on this level
16:23 CIA-15 bioclipse: jonalv * r4047 /trunk/plugins/org.eclipse.nebula.widgets.grid/: Initial import.
16:23 CIA-15 bioclipse: jonalv * r4048 /trunk/plugins/org.eclipse.nebula.widgets.grid/ (10 files in 5 dirs): Initial import.
16:24 CIA-15 bioclipse: jonalv * r4049 /trunk/plugins/net.bioclipse.statistics/ (3 files in 3 dirs): Changed to use the jar file i org.eclipse.nebula.widgets.grid instead
16:31 CIA-15 bioclipse: jonalv * r4050 /trunk/plugins/net.bioclipse.statistics/ (3 files in 3 dirs): reverted into using the jar file in the project again. Things didn't work. Will look at this again at some other time.
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